[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned synthetic sample PX-01, return the - strand from px_core_A coordinates 91 through 114.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Select a specific sequence region by genomic coordinates (start-end position), highlighting it in the genome view. This sets the region as the active sequence selection, useful for subsequent operations like copy, extract, or analysis.

Export genome features in BED format for visualization and analysis

gene CDS exon tRNA rRNA misc_feature regulatory repeat_region all

Save a named genomic position or region bookmark for quick navigation later. Use this when the user asks to bookmark, pin, flag, or save a specific coordinate range. This stores only the genomic interval, not track visibility or full workspace layout.

Navigate to specific genomic coordinates in the genome browser to VISUALIZE the region. Use this when users ask to "show", "display", or "view" a genomic region by coordinates. Coordinates are 1-based base pairs; the chromosome defaults to the one currently displayed, so pass chromosome only when the user names a sequence that is actually loaded. For gene-based navigation, use jump_to_gene instead. For retrieving raw sequence data, use get_sequence instead.

Run BLAST on a sequence extracted directly from a loaded genome chromosome region.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned synthetic sample PX-02, return the + strand from px_core_B coordinates 218 through 242.

Design a forward and reverse primer pair to amplify a target DNA sequence. Use upstreamBp/downstreamBp when the amplicon must include flanking bases; both are interpreted relative to gene strand, so reverse-strand upstream is higher genomic coordinates and reverse-strand downstream is lower genomic coordinates. Provide at least 150bp of sequence, or use geneName or chromosome/start/end to fetch it.

Export sequences from the current genome view in FASTA format

all genes cds intergenic features_only background_only

gene CDS tRNA rRNA misc_feature regulatory


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned synthetic sample PX-03, return the + strand from px_core_A coordinates 345 through 370.

Calculate GC content for a chromosome coordinate range from the currently loaded genome. Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned synthetic sample PX-04, return the - strand from px_core_B coordinates 472 through 498.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned synthetic sample PX-05, return the + strand from px_core_A coordinates 599 through 626.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned synthetic sample PX-06, return the + strand from px_core_B coordinates 726 through 749.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned synthetic sample PX-07, return the - strand from px_core_A coordinates 853 through 877.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned synthetic sample PX-08, return the + strand from px_core_B coordinates 980 through 1005.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For synthetic neighborhood audit PX-156, find tRNA features within 1265 bp of px_core_B:8241.

Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position, genes around a location, or what is nearby a genomic coordinate. NOT the same as navigate_to_position which moves the view, or list_annotations which lists all annotations in a region.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Searches for a regular expression or nucleotide pattern across a specified genomic region.

Search for genomic features by ANNOTATION TEXT, FUNCTION KEYWORD, or FEATURE TYPE (e.g., find all tRNA, all kinase-related CDS, all transport proteins). This is a BROAD search across all feature types. Do NOT use this to look up a specific gene by its name — use find_gene_by_name or jump_to_gene instead.

Get predicted operon structures for a chromosome from loaded annotations. Returns operon coordinates, strand, gene count, member genes, and length. Use this when the user asks to show, list, find, predict, or inspect operons in the current genome.

Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For synthetic neighborhood audit PX-157, find CDS features within 1272 bp of px_core_A:9204.

Export coding sequences (CDS) in FASTA format

Search for binding sites of a primer sequence within a template, with scientific mismatch tolerance. Uses position-dependent scoring (3' end weighted), nearest-neighbor thermodynamic Tm estimation, and configurable filtering. Finds both forward and reverse-complement binding sites.

Find genes associated with a specific metabolic pathway

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For synthetic neighborhood audit PX-158, find CDS features within 1279 bp of px_core_B:9341.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For synthetic neighborhood audit PX-159, find CDS features within 1286 bp of px_core_A:10304.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For synthetic neighborhood audit PX-160, find CDS features within 1293 bp of px_core_B:10441.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For synthetic neighborhood audit PX-161, find tRNA features within 1300 bp of px_core_A:404.

Export genome features in BED format for visualization and analysis


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For synthetic neighborhood audit PX-162, find CDS features within 1307 bp of px_core_B:541.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For synthetic neighborhood audit PX-163, find CDS features within 1314 bp of px_core_A:1504.

Export genome annotations in GFF3 format


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Produce the validated reverse complement for synthetic oligo PX-187: CCGGGCGAGGCTGGGGACTATTAGGGAGCT.

Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).

Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.

Calculate biochemical properties like melting temperature (Tm), GC content, and length for a given DNA primer sequence (18-35 bp). Use this to check if a sequence is suitable as a PCR or sequencing primer.

Paste the current sequence clipboard at a specified genomic insertion position. Set reverse_complement=true to reverse-complement the clipboard sequence before it is pasted. Requires a previous copy_sequence or cut_sequence call. This creates a queued sequence-editing Action; execute_actions applies the queue.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Produce the validated reverse complement for synthetic oligo PX-188: CGCACATAGCAAAGATTGGTGTGGGTCTTAT.

Validate a plugin for compatibility and errors

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Produce the validated reverse complement for synthetic oligo PX-189: TTGGACCAAAAAACCCAGGGGATAATGTTAGG.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.

Validate a local BLAST database integrity and format


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Produce the validated reverse complement for synthetic oligo PX-190: CGTGTGGGTTGAGACGCGCCGTGG.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Produce the validated reverse complement for synthetic oligo PX-191: CACAGCGGCGCCGATATGTGTCCCA.

Execute all pending sequence-editing Actions and generate a modified GenBank file. This executes queued genome edits only; it does not run checklist Tasks. Reverse-complement paste_sequence and insert_sequence Actions are converted before they are applied.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Produce the validated reverse complement for synthetic oligo PX-192: GACTCTCTATCCATCGACCCTACATG.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Produce the validated reverse complement for synthetic oligo PX-193: ACCTTGGAAGGGTAAGACCTGCTTCCG.

Predict promoter regions in DNA sequence

Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Produce the validated reverse complement for synthetic oligo PX-194: GTCTAGCCTCATCGGCAACGGACCCTAT.

Search for binding sites of a primer sequence within a template, with scientific mismatch tolerance. Uses position-dependent scoring (3' end weighted), nearest-neighbor thermodynamic Tm estimation, and configurable filtering. Finds both forward and reverse-complement binding sites.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Using the bacterial code, translate synthetic CDS PX-218 in frame 1 and retain stop symbols: ATGACCGACGCTGAATTCCGTAACTAA.

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

standard vertebrate_mitochondrial bacterial archaeal

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.

Get predicted operon structures for a chromosome from loaded annotations. Returns operon coordinates, strand, gene count, member genes, and length. Use this when the user asks to show, list, find, predict, or inspect operons in the current genome.

Create BLAST protein database from loaded genome using 6-frame translation

Stop the currently running benchmark. Gracefully terminates the benchmark execution and saves any partial results collected so far.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Using the standard code, translate synthetic CDS PX-219 in frame 1 and retain stop symbols: ATGGACGCTGAATTCCGTAACGGTCAATAA.

Export coding sequences (CDS) in FASTA format

Export protein sequences translated from CDS in FASTA format


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Using the bacterial code, translate synthetic CDS PX-220 in frame 1 and omit stop symbols: ATGGCTGAATTCCGTTAA.

Create a new plugin from template or code


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Using the standard code, translate synthetic CDS PX-221 in frame 1 and retain stop symbols: ATGGAATTCCGTAACGGTTAA.

Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Using the bacterial code, translate synthetic CDS PX-222 in frame 1 and retain stop symbols: ATGTTCCGTAACGGTCAATATTAA.

Load operon definition files (JSON/CSV/TSV/TXT) directly with file path specification or via file dialog. Supports RegulonDB TSV format.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Using the standard code, translate synthetic CDS PX-223 in frame 1 and omit stop symbols: ATGCGTAACGGTCAATATAAACTGTAA.

Start a resumable Deep Gene Research job bound to an exact CodeXomics feature target; it never writes annotations directly.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Using the bacterial code, translate synthetic CDS PX-224 in frame 1 and retain stop symbols: ATGAACGGTCAATATAAACTGACCGACTAA.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Using the standard code, translate synthetic CDS PX-225 in frame 1 and retain stop symbols: ATGGGTCAATATAAATAA.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Measure Shannon sequence complexity for synthetic sample PX-280: ATAGAACAGTGGCCGGCGCATATG.

Paste the current sequence clipboard at a specified genomic insertion position. Set reverse_complement=true to reverse-complement the clipboard sequence before it is pasted. Requires a previous copy_sequence or cut_sequence call. This creates a queued sequence-editing Action; execute_actions applies the queue.

Copy a sequence region into the sequence-editing clipboard and queue a copy Action. This is not a checklist Task. Use paste_sequence after this to queue a paste, and execute_actions(auto_save=true) to apply queued sequence-editing Actions.

Detect whether a sequence is DNA, RNA, or protein

Perform BLAST search on a DNA sequence

Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Measure Shannon sequence complexity for synthetic sample PX-281: ACTCGAAAACAAACATCGTAGATCC.

Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.

Perform BLAST search on a DNA sequence

Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.

Run BLAST on a sequence extracted directly from a loaded genome chromosome region.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Measure Shannon sequence complexity for synthetic sample PX-282: GGGTACACGTTATCCTTTCCTCAACG.

Perform BLAST search on a DNA sequence


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Measure Shannon sequence complexity for synthetic sample PX-283: TGGGCTGAACTGTAGTGGAAGGTTGTT.

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.

Perform BLAST search on a DNA sequence


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Measure Shannon sequence complexity for synthetic sample PX-284: CAAACGGAGCATGTGAGCTGGACTCACT.

Queue deletion of a sequence region as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Measure Shannon sequence complexity for synthetic sample PX-285: ATGCACAGTCTGCCTATCGCGGATCAGTA.

Perform BLAST search on a DNA sequence


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Measure Shannon sequence complexity for synthetic sample PX-286: GTCTGAACATCGGAGTCGGGCCTTCCGCCA.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Measure Shannon sequence complexity for synthetic sample PX-287: CGCTATGCCACCCAAAAGTTCCGTGACAAGT.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Calculate the dna molecular mass for pinned sample PX-311: GGTAAGCCGTGATAACCCCTCTCGACCT.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.

Analyze codon usage patterns in DNA coding sequence with comprehensive statistics and visualization. Supports analysis by direct sequence input, gene name, or locus tag.

Analyze protein domains, families, and functional sites using InterPro database. Provides comprehensive domain architecture, functional annotations, and evolutionary relationships.

Pfam SMART PROSITE PANTHER PRINTS Gene3D SUPERFAMILY PIRSF HAMAP CDD NCBIfam SFLD SignalP_EUK SignalP_GRAM_POSITIVE SignalP_GRAM_NEGATIVE Phobius TMHMM


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Calculate the protein molecular mass for pinned sample PX-312: MCDEFGHIKLMNPQRSTVWYGAVLIPFYWST.

Open an interactive 3D protein structure viewer from cached data, a local PDB file, an online PDB URL, a UniProt/AlphaFold accession, a PDB ID, or a gene name. Online structures are downloaded automatically.

chain secondary atom residue temperature

Export protein sequences translated from CDS in FASTA format

Perform BLAST search on a protein sequence


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Calculate the dna molecular mass for pinned sample PX-313: TTCTGCAATTTCCGATGCGAGCATCAATTA.

Calculate biochemical properties like melting temperature (Tm), GC content, and length for a given DNA primer sequence (18-35 bp). Use this to check if a sequence is suitable as a PCR or sequencing primer.

Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Calculate the protein molecular mass for pinned sample PX-314: MEFGHIKLMNPQRSTVWYGAVLIPFYWSTCM.

Download protein 3D structure from PDB database by PDB ID or gene name. Retrieves experimental structures with resolution data.

Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.

Create BLAST protein database from loaded genome using 6-frame translation


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Calculate the dna molecular mass for pinned sample PX-315: GGAGTGCAGTTTGTGGGAACTGTGCGACTCCC.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Calculate the protein molecular mass for pinned sample PX-316: MGHIKLMNPQRSTVWYGAVLIPFYWSTCMNQ.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Calculate the dna molecular mass for pinned sample PX-317: GTTAGGCTAAGAATTCCTACCTTAT.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Calculate the protein molecular mass for pinned sample PX-318: MIKLMNPQRSTVWYGAVLIPFYW.

Get detailed protein information from UniProt


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Compute primer properties for synthetic assay PX-342 using oligo CACTACCCGTCGCAATAAC.

Delete primers from the library. Requires confirm=true. Optionally scope to one chromosome to remove only pinned placements there.

Search for binding sites of a primer sequence within a template, with scientific mismatch tolerance. Uses position-dependent scoring (3' end weighted), nearest-neighbor thermodynamic Tm estimation, and configurable filtering. Finds both forward and reverse-complement binding sites.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Compute primer properties for synthetic assay PX-343 using oligo CATTGAGTAGGGCGGAGCGC.

Save a primer oligo to the primer library (stored separately from the genome, never written into the genome file). Binding sites are predicted automatically; provide chromosome/start/end only to pin a specific manual placement.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Compute primer properties for synthetic assay PX-344 using oligo ACACCACAACGACAGAGTGAC.

⚠ DEPRECATED: This tool is deprecated. Use 'analyze_interpro_domains' instead. This tool name exists only for backward compatibility and will be removed in future versions.

List primers in the library and their binding sites (pinned + predicted) for the current chromosome, optionally filtered by genomic interval.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Compute primer properties for synthetic assay PX-345 using oligo GTAGAACTTAAACGTAGTAATG.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.

Design a forward and reverse primer pair to amplify a target DNA sequence. Use upstreamBp/downstreamBp when the amplicon must include flanking bases; both are interpreted relative to gene strand, so reverse-strand upstream is higher genomic coordinates and reverse-strand downstream is lower genomic coordinates. Provide at least 150bp of sequence, or use geneName or chromosome/start/end to fetch it.

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.

Analyze codon usage patterns in DNA coding sequence with comprehensive statistics and visualization. Supports analysis by direct sequence input, gene name, or locus tag.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Compute primer properties for synthetic assay PX-346 using oligo TTAGGCAGCGCGTATCTT.

Analyze protein domains, families, and functional sites using InterPro database. Provides comprehensive domain architecture, functional annotations, and evolutionary relationships.

Calculate GC content for a chromosome coordinate range from the currently loaded genome. Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Compute primer properties for synthetic assay PX-347 using oligo ATTAAGTCAGGTAGTCAGT.

Calculate biochemical properties like melting temperature (Tm), GC content, and length for a given DNA primer sequence (18-35 bp). Use this to check if a sequence is suitable as a PCR or sequencing primer.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Compute primer properties for synthetic assay PX-348 using oligo TTGCACGAGCCACCAAGGAA.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Compute primer properties for synthetic assay PX-349 using oligo AGCCCTTGCCGTACCAATTAG.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the explicit synthetic template in assay PX-373 for exact sites of primer CCTCGCCAGCCTTCGTGTAC, allowing zero mismatches. Template: ACATTCAGCCTTAAGTAGGTCGTCCAGTAACATTCATATAGCTGAAGCAGGTACTCCAAGACCCCGTTCCAGTTATTAGTACTGGCTGACCGGCTTCAGGGAGCCTGCCTGGACAGGTGCAATCTGTAGCTGATCACTGCTCTTAAGCTCGTCGCTGATGGAAGATTTATCAGCTGTTCCGCGAGTAGAAGGAATCAGCCAACCGATCGATGCGGCTAGACTAACATCCACATGATCTTCATTGACTCTCAAGACGATAGGCGTAATATTCAATAGTAGAAGACCCCGGCGACGAGACTCGATAGAGCCCGGTCAGGGTGTCGGTGGCGGCAGCAGGCGGAGATCATTGTCGGACTCCATAGCCCACGTCCATAAGTGGAGGGCCTCGCCAGCCTTCGTGTACATAATCCGATCACGG

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.

Search for specific sequence motifs or patterns within genomic regions. Supports exact matches, IUPAC ambiguity codes (N=any, R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=not A, D=not C, H=not G, V=not T), regular expressions, and mismatch tolerance.

Locates recognition and cleavage sites for restriction endonucleases in a genomic region. Supports 80+ enzymes with IUPAC ambiguity codes, staggered cut positions (5' overhang, 3' overhang, blunt end), and HF variants.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the explicit synthetic template in assay PX-375 for exact sites of primer AACGATTGCCGCGTAGTAGCGC, allowing zero mismatches. Template: TGCGTAGACACTCGACCGAGTTTTGGAGAGGTAGAGATCGGGCAGGCGTCCCACGTAAGGAGATTTCCCTGGTACCAAAAGGAGTGTCAACCGTTCCCTACATGGGTGGTAGTAGATAGAGGCTGTTTTGCCGAAAATTAACCTCTCGTCGCCGTTGCACTGCGGTATCAATTAGGGATATTTATAGTACCCCAGGAGACTAGCACAGCTGAATACGGACGGTAGGTACCATGCCTCCAACATGGCCGGAGTTATATCTTAGTGTTGCCCTACAAGCTGGTGATCCAAGTTCCGCACGTCACGGCGAAGGACTCGGCGTATAGAAGCACATCTGAACCCTAGCCACGAGACTTACCCGTAGCCCCCAGTAGCAATTACCCAGATAAACGATTGCCGCGTAGTAGCGCTTCTGCTGTAGTACCAT

Search InterPro database for domain families, functional sites, and protein signatures using keywords, names, or descriptions. Enhanced with advanced filtering and batch processing capabilities.

name description keyword signature go_term literature all

Pfam SMART PROSITE PRINTS PANTHER Gene3D SUPERFAMILY PIRSF HAMAP CDD NCBIfam SFLD

Search for genomic features by ANNOTATION TEXT, FUNCTION KEYWORD, or FEATURE TYPE (e.g., find all tRNA, all kinase-related CDS, all transport proteins). This is a BROAD search across all feature types. Do NOT use this to look up a specific gene by its name — use find_gene_by_name or jump_to_gene instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the explicit synthetic template in assay PX-377 for exact sites of primer CTGTCCACGAATCGCTCAC, allowing zero mismatches. Template: AGTCTAGAGACATGCGCTTCATACAGGCAATCTTCGCGGCGTGTAACTGGACAATTTGGCGGCCAGCTATAGGCACCAGCGTCACTAAAAGTCACGGTCTAGTCTACAGAGCTTCCAACCACGTTCACGTGAAATTCATTTTGCAGAATCCGCGAGCCCGTAATGACGAAAGTGTGTTACACGGCGAGCTCGAGAAAACCAAAGATAGCCAAAACAGAGAGCCTCGGTGCGGACAACGTATGGACTTGTAACAAGTTTCTTGCACGAATATATCTCGCAAATTACGCGCTTTTGGCGACCCGGGACACCTCAACATGACTACTAGATCCGGGGACAAAGGCACTACACCTATGCCGGTGGGCCCTAGGACTTTGGACACAATTGTCGCTGTCCACGAATCGCTCACGCATGTGGAATTCCA

Search for binding sites of a primer sequence within a template, with scientific mismatch tolerance. Uses position-dependent scoring (3' end weighted), nearest-neighbor thermodynamic Tm estimation, and configurable filtering. Finds both forward and reverse-complement binding sites.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the explicit synthetic template in assay PX-380 for exact sites of primer AGTAGAAGAGATTGATCAGCGG, allowing zero mismatches. Template: TTCCAGTAAGCTTCCACTACCTCCTAGTCTCCGCATTAAGGTGATCCCGATCCATTCCCGTACCAGCCTTCGTCCGAGACCTCAATTAAGGCGGTTTCGTCTTTGCTTATGCCAGAAAGATGATGTAAGCTTCGGTGCCCGGAGTGGTCGTTGGCTTTGGAGCTGCATGCATTTACCAGAACTGAGATGCTTAAGGTCCAGATAGTTTTTAGACCACATCTCTTCAAGACATTGAATGGTATACGCCTATCACACTTATGGCGGCTCGATACGACTACTGCACACATTAATGACACAATCCTAAGCTGCTAACGGCCGTTTTCTAGTCACCCGGGCCGGCCTACAGCATGCAGTAGTCTAGATACCGTCGTAAAAAAGCACGCGTCTTATAGTAGAAGAGATTGATCAGCGGCAGTGCTCGCCGAGTCCT

Search AlphaFold database for protein structures by gene name. Returns predicted 3D structures with confidence scores and metadata.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Virtually digest the explicit synthetic molecule for check PX-435 with HindIII and PstI: TTGGCCTGCCACCTGCGTGGCGGCTCGTATGTTGACAAGTATAAGGCATTTACCGTGTCATGCTTACCTGGGAAAAAGACAGGATAGGTCAGCCACAAATCGCGCAAATGCCGCGCTGGTTAACAATCACGGCTTGTTTGCGTCGGAGTAGCAACTATGTCCGCTGAAAGTACAATAGAAGTCGCATGATGACTGGGACCGTCATCACACTCGGTCAGATTACTGTTTCTTCCCCCTGATTTAAACTCATCTTGAGCGTGGCGCAACCACAGGGCGACATTGCCTAAGTCCACCTCAGAGCTGGAAATAGGTATCCATGTGTAATTGGAGAGGGCCAGAGGGAATAGTGGAGTATGTGTCCGATGGTTGGCCCTGAAGTGTGCTAACCGACGATCCCGGTGTTCTTTGAGTAAGAACGTGCTGCAGATGAGCTGGACCGGGACGGCCTCTGAAGCTTAAAGTACGCTATGCTCTGCAGATCGATCCAACGCCGATCCAA.

Performs an in-silico restriction digest of a chromosome or sequence using one or more restriction enzymes. Calculates fragment positions, sizes, end types (5' overhang, 3' overhang, blunt), and provides digest map for gel electrophoresis visualization.

Simulate agarose gel electrophoresis to visualize restriction digest fragments. Renders DNA bands on a virtual gel. This is a visualization-only tool — it does NOT perform digestion. Call virtual_digest first and pass its fragmentDetails to this tool.

Get the current content of the sequence clipboard. The clipboard holds sequences that have been copied or cut from the genome using copy_sequence or cut_sequence. Use this to check what sequence is currently stored in the clipboard before pasting or to verify a copy/cut operation. NOT the same as get_action_list which lists pending editing actions.

Validate a local BLAST database integrity and format


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Virtually digest the explicit synthetic molecule for check PX-436 with XhoI and NotI: TCTGCTAGCTTGAGCCGTAGGGACGTGCTGATATCTGCCTATTGGCAGATAACATGGTAATGAATCACTCTACGTCTGTCTGCATCAACAACTCGCGAGTCGCGCTCCACCTATATTAGTGCCGACGTCCCGTCAATAGAGCTCCTCTTCGTGCGGAGCAGCATTTGTTATGAGCATATCCGCAAACTTAAATGCAAACCAGGCTTAGTTAGGAAAACTGATTCTACGACGTATAATGAATGCCTCTGGTGCCCTGGAACAAATCGTCAGTGTGTGCGCGACTACTTGCAAAACTACCAGAGATGAATGGCGTTGGGATCATGCAAAAACTCAACCCACTCGGCGGCGAGCCGAATACTCAGTCACTTCTGGAGGTGTCGCTTGTGCCCATGCATCTATGTTCATCACATAAAGCCAATGTGAGGGTGTTAATACCCTAGTGAGTCTACTGGCTCGAGCACCCTTTCCCCGCATGCGGCCGCATCTAATTGGTGCGCGTGCAAA.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Virtually digest the explicit synthetic molecule for check PX-437 with PstI and EcoRI: AGACATACAGCCAGGGTGAATTCTTCCCTTATCGACGCAGAAGGATGCCTGGTACCGCAGATTTCTTACTAGGGTGCAGTAACTTGAGGCATGCCGCAGGAGCCGAAACGCGTGATACGGTGTTGCCCCAGAAATTAGGAGGTCCAATCGGGTCGAGCCCTACACTCCGTCTCCACCGCTTGGTTGCCGGTAACCCGATCCAATGGGGAAACCGGGAGCGATAATACTCTGCAGATCTAAGACTTGGAGGCTTAGAATAAGGTTAACACTACAAAAACTATGAATGCAAGACCGCATGCGAGAATGTAAATCTCGCGCGACCAGAGTTACAACCCATTTGGTGAAAGTGAACTACGTATGGAAACTTCCAAGCTAGGTCTTAAGTACGGACATGGCTAGTCAGTGTGAAGATTGTCAGGCCGGTATCGACATCACACCGACCCCAAAAGGCACCTGCAGTTTACCGAATCTTGAATTCGAGGGGCGTACCTGGGCCCCGCG.

Searches for a regular expression or nucleotide pattern across a specified genomic region.

Calculate GC content for a chromosome coordinate range from the currently loaded genome. Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Virtually digest the explicit synthetic molecule for check PX-438 with NotI and BamHI: TCATCGGCTGCCTTATCTGTGCTAGCTGACCCTAAACACCGTCACCTTACGCTCTTCGGCAAAAAAAACGGAATAGATGCAATTCCGAAGTATTATAGCAACCCGCTTATCCGGGCTTGGAGTCACGTGTTCAACAAGATAAAGACACAGCACGAGTTGTATGATAGCAGACTATCTCCTGCCCGTGTCACGGAAAATGAAAGGCGCCATGGAGTTCACAACCCTGCGCCCCCGCGCTAGGAAGGTAGAGCAGTAATAAACGACTTCTTAGCGCTGGGCCTTGCGAGGACGAAAACCGGGAACAGCGTCCACATCGTGGCATTAGGACATTTCACCAGGTCACGGAAACGAGCCTTGTACAGGTGGCGCCGCGTTGTATCGTAGCTGATCACAGAAAATACTGTCGAGTAAATAACGTGAAATAAAGTGCCCAGCTGTACGTGCAAAGTGTCTGGCGGCCGCTACGTAACTGCTCGGGATCCTCCTAATGTTGCGGATTTTACCAC.

Load sequencing reads files (SAM/BAM) directly with file path specification or via file dialog

Get the current status of the benchmark system, including initialization state, whether a benchmark is currently running or paused, and how many test suites are loaded.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Virtually digest the explicit synthetic molecule for check PX-439 with EcoRI and HindIII: AACTGGTGCTTAGCCGCCCTGTCGTACAGTAGTGCTCACGTAGAGCGTTTCGGTGGCCGATACCCCAGCGAGCTTGGCTAGCATTGTACTGGTTAGGAACTATAGTCAGGTATGTCATCTGCGCTTTGTGCCAATGAACGGAGACATCTCGAGCTAGAACTTTCGACGCAAAGCTGAGCAGGCGCGGGCTCTGTTACCATTCAGTCATGACCGGCTGTGCCCTCATGCAAACTGAGCTGCCCTTAGCTTATTGCTTTATGTATAGCGGTTAACCCTGGCTCCCAATACCGTTTGTGTTGGTAAATTGACAGCCCCCCACTCAGTCCATATCACATCGTGTCCGCTACTCCGGATTTAATTTTCACATGCAAGTCCGCGCGGGCTTGTATCTTCCACAGTCATCGGGAACTATCGGTGTCGACTAGGGATGTCGTCGTTACCTGTGGGAAACCCTAGAATTCTTGTTGCCTGAGAAGAAGCTTCACACCCAGACACCTCCAG.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Locates recognition and cleavage sites for restriction endonucleases in a genomic region. Supports 80+ enzymes with IUPAC ambiguity codes, staggered cut positions (5' overhang, 3' overhang, blunt end), and HF variants.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Virtually digest the explicit synthetic molecule for check PX-440 with BamHI and XhoI: CAATTTGTCGCTGCCCTCCCTCTATGCTTTTGTTAGGTAAGGCCTGCTAAATACGTTACGCCGCGAGCACGTTCTTTGCCTTCCGTCTATCTCCACGGCTGCGGTTCTTGTGGCCCGGACCCATGACTCCAATAGTCCGCAGACTAGCCCCAACCAAGACGAAAATCTTAGGCAATGCAACAGACTCCGGAAAGCGAATGCGCCGCCATATGGGCATAGATCGTCTCCTCAGAACAGATAACTTGATTACCCATGTGCCATATTACTCACTTCAAAAGTTGACCGACAATTCCTTCCTTGTTGGCGTGCGTATCAGCCTGGTGGAACAACACTCTAGTGCGATGTTAACTGATAGGAGACACAGGGAATAGCCAAAGATTCGCCACCACCCAGAAGCGCTTCTTGGATCCCCTCTCGATGTTTTCACAGCAGTACGGAGGCACCGGACTCGCTGGAGGATCCAGGGGCAGTGTCTTCGCTCGAGATTATGGCATTTTATAGCGC.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Virtually digest the explicit synthetic molecule for check PX-441 with HindIII and PstI: GCCTACCAGCCCACTAATAAGGATAGCAGGGACGGACATACCAGCGATGCGCGACCCTCAAAGAAATCGAATGGGTCATCCTAAAGAGCGCCTCAACTTGACTGGGAAAACTGTACCGCGGAGCTTCGAGGAGGTTCCATTTTGTATGAATGACCTGGTCACCATGCTTCCGTGTGGCTTGTATCACGCTACAACTACCAAATGAGGTGAGAGGTGCTCACATTATCTCTATTAAACACACGGACCGGTTTAAGTGTCCGTAATTCAATTTGATAGTTCACCCCCGCTGTACGTGGAGGTAATGACGCCGTTAGTAATAGGTCTATTGGATTGCAAAGGCGAAAGGAAGGGACTAGCATTGGAGCGGGAGCACATCGCATATCACGGCTCCTCCTAGTAGGACGCCAGGCGTTGGGAAGTCCCTACAGCCGATCCCAATGTAGCGAATGGCATCCGTAAGCTTAGTGCGGAGCGCGCTGCAGGCTGGGCTGTAGCTTGGCAAA.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Virtually digest the explicit synthetic molecule for check PX-442 with XhoI and NotI: ACCTGAACGCGGATTCAAGGTACAAGTGAAGATTGGCAAGTCAACGTACACTCGATCTATGATGAAGTGCCTGAGAGCGGGCGTGTCGGTGCATACTGGCTTAGGTTTTTCAGCGCCAAGTCTAGGCCATATAATACCGAGAATACTATTGTGTCTTGATTGTGGTGAAACCTGTAGCTGCATAGCGGGGAATTCCTGGGAAAGGAATAGGTATGTGGCTTGTTTGCCGATTATAGTCCTTACCCGATCTCAGCGAGCACACCGCCGAGTAGGGATTATGTAACACGGAATCCAAAAAACATACACGCGATCGCCCAAAAGCTGGGACAGACGCACGATTAGTTAGTGCCGGCGAAGTCAGGTCGTAATCATATTGCATTATCCGCAGAGCTGCTCGACACTCGCAACATTAATTTCGTTGGAAGGGAGCATCTATGGCTCAGGAACGAATGAAAGCACTCGAGCCGAAGCCGCTTAAGCGGCCGCTATTTGAGTGGTCCTGCGAAAA.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] From the pinned enzyme catalog for audit PX-466, list commercial entries matching XhoI with recognition lengths 4-10.

List available restriction enzymes from the built-in database (80+ enzymes). Supports filtering by name query, recognition sequence length, overhang type (5' overhang, 3' overhang, blunt), and commercial availability. Also shows isoschizomers and HF variants.

Get the list of all chromosomes (contigs/scaffolds) in the currently loaded genome, including their names, lengths, and which one is currently selected. Use this when the user asks about chromosome names, genome contigs, scaffold list, or wants to know what chromosomes are available.

List all available tools in the system, organized by category. Use this to discover what functionality is available or to get help with available commands.

List all available plugins in the system, including installed, enabled, and marketplace plugins. Provides comprehensive plugin information and status.

all installed enabled disabled available outdated

name version status last_used popularity


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] From the pinned enzyme catalog for audit PX-467, list commercial entries matching PstI with recognition lengths 4-10.

List current tasks in the workspace task tracking system, optionally filtered by status.

all pending in_progress completed failed


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] From the pinned enzyme catalog for audit PX-468, list commercial entries matching NotI with recognition lengths 4-10.

Display the Action List Manager interface for queued sequence-editing Actions. Actions are genome edit operations, not checklist Tasks.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] From the pinned enzyme catalog for audit PX-469, list commercial entries matching EcoRI with recognition lengths 4-10.

List all positional highlights currently shown for the active tab, including each highlight's id, chromosome, start/end coordinates (1-based inclusive), length, label, and color. Use this to review what is highlighted or to obtain an id before calling remove_highlight.

List available DNA markers/ladders from the built-in commercial marker database. Covers NEB, Thermo Fisher, Takara, and common Chinese domestic brands (TransGen, Vazyme, BioMaded, Sangon). Supports filtering by brand, category, and text search.

List primers in the library and their binding sites (pinned + predicted) for the current chromosome, optionally filtered by genomic interval.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] From the pinned enzyme catalog for audit PX-470, list commercial entries matching BamHI with recognition lengths 4-10.

Get list of all currently loaded files in the genome browser with their complete paths and metadata

List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] From the pinned enzyme catalog for audit PX-471, list commercial entries matching HindIII with recognition lengths 4-10.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] From the pinned enzyme catalog for audit PX-472, list commercial entries matching XhoI with recognition lengths 4-10.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] From the pinned enzyme catalog for audit PX-473, list commercial entries matching PstI with recognition lengths 4-10.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-474
Objective: filter the pinned enzyme index by the supplied catalog constraints.
Pinned inputs: {"query":"NotI","minRecognitionLength":4,"maxRecognitionLength":10,"commercialOnly":true}.
Do not substitute values from another genome or external service.

Quickly create BLAST databases (both nucleotide and protein) for the entire currently loaded genome. Use this as the default/quick way to index the genome when no specific chromosome name is specified. Automatically associates databases with the genome for smart database selection.

Create BLAST protein database from loaded genome using 6-frame translation

Get comprehensive information about the loaded genome including chromosomes, annotations, statistics, and metadata. Use this to understand the available genomic data.

Filter BLAST search results by identity, E-value, coverage, or hit count. Defaults to the most recent BLAST search, so the filter criteria are usually the only arguments needed.

Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 从固定酶目录中筛选名称匹配 EcoRI、识别长度为 4-10 且可商购的条目（PX-475）。

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Navigate to specific genomic coordinates in the genome browser to VISUALIZE the region. Use this when users ask to "show", "display", or "view" a genomic region by coordinates. Coordinates are 1-based base pairs; the chromosome defaults to the one currently displayed, so pass chromosome only when the user names a sequence that is actually loaded. For gene-based navigation, use jump_to_gene instead. For retrieving raw sequence data, use get_sequence instead.

Locates recognition and cleavage sites for restriction endonucleases in a genomic region. Supports 80+ enzymes with IUPAC ambiguity codes, staggered cut positions (5' overhang, 3' overhang, blunt end), and HF variants.

Get the current state of the genome browser including position, visible tracks, loaded data, and session information. Use this to understand the current context before making other operations.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Explain what GC content means without running any analysis.

[Assistant] GC content is the percentage of guanine and cytosine bases in a DNA sequence.

Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.

List all available plugins in the system, including installed, enabled, and marketplace plugins. Provides comprehensive plugin information and status.

Get the current status of the benchmark system, including initialization state, whether a benchmark is currently running or paused, and how many test suites are loaded.

Analyze codon usage patterns in DNA coding sequence with comprehensive statistics and visualization. Supports analysis by direct sequence input, gene name, or locus tag.

Calculate biochemical properties like melting temperature (Tm), GC content, and length for a given DNA primer sequence (18-35 bp). Use this to check if a sequence is suitable as a PCR or sequencing primer.

Get the current content of the sequence clipboard. The clipboard holds sequences that have been copied or cut from the genome using copy_sequence or cut_sequence. Use this to check what sequence is currently stored in the clipboard before pasting or to verify a copy/cut operation. NOT the same as get_action_list which lists pending editing actions.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Show me an example of how a region navigation request could be phrased, but do not navigate.

[Assistant] For example: Navigate to positions 1000 through 2000 on the active chromosome.

Zoom the genome browser view to fit a specific gene, centering on it with configurable padding. This changes the visible region to show the entire gene with surrounding context. Use this when the user asks to zoom to a gene, focus on a gene, center view on a gene, or fit a gene in view. NOT the same as select_gene which only highlights without zooming.

Calculate GC content for a chromosome coordinate range from the currently loaded genome. Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.

Save a named genomic position or region bookmark for quick navigation later. Use this when the user asks to bookmark, pin, flag, or save a specific coordinate range. This stores only the genomic interval, not track visibility or full workspace layout.

Add a persistent visual highlight (a colored box) over a genomic region, spanning the full height of the ruler and tracks. Unlike select_sequence_region (which sets a single active selection for copy/extract), this supports MULTIPLE and OVERLAPPING highlights that stay visible while panning and zooming. Use when the user asks to "highlight", "mark", or "box" a region so it stands out. Each call adds one more highlight; use clear_highlights to remove them all or remove_highlight to remove one.

Select a specific sequence region by genomic coordinates (start-end position), highlighting it in the genome view. This sets the region as the active sequence selection, useful for subsequent operations like copy, extract, or analysis.

Switch to a specific tab in the browser interface by tab ID, name, or index position


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Go to the gene.

[Assistant] Which gene name or locus tag should I navigate to?

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.

Delete a genome annotation by identifier (locus_tag, gene name, or protein_id) with change tracking. Use this when the user explicitly asks to delete or remove a specific annotation. NOT the same as delete_sequence which removes sequence data.

Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Extract the sequence from that region.

[Assistant] Please provide the chromosome and start/end coordinates, or select a region first.

Queue deletion of a sequence region as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.

Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Infer a maximum-likelihood phylogenetic tree with IQ-TREE.

[Assistant] No IQ-TREE execution tool is available in the current CodeXomics tool catalog.

Jump directly to a gene location by gene name or locus tag. This is the PRIMARY tool for navigating to genes when you know the gene name.

Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.

experimental homology predicted uncertain


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 只解释什么是反向互补序列，不要调用工具。

[Assistant] 反向互补序列是先将碱基替换为互补碱基，再反转序列方向得到的序列。

List all available tools in the system, organized by category. Use this to discover what functionality is available or to get help with available commands.

Get the benchmark results history. Returns statistics from all previous benchmark runs, including success rates, test counts, durations, and the latest run details.

Load annotation files (GFF/BED/GTF) directly with file path specification or via file dialog

Get the current state of the genome browser including position, visible tracks, loaded data, and session information. Use this to understand the current context before making other operations.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 请给出引物设计的一般步骤，但现在不要实际设计。

[Assistant] 通常需要确定目标区域、设置长度和退火温度范围、检查特异性，再评估候选引物。

Navigate to specific genomic coordinates in the genome browser to VISUALIZE the region. Use this when users ask to "show", "display", or "view" a genomic region by coordinates. Coordinates are 1-based base pairs; the chromosome defaults to the one currently displayed, so pass chromosome only when the user names a sequence that is actually loaded. For gene-based navigation, use jump_to_gene instead. For retrieving raw sequence data, use get_sequence instead.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.

Load genome files (FASTA/GenBank) directly with file path specification or via file dialog


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned locus fxg01, find its coordinates without navigation, retrieve exactly that returned interval, then translate the retrieved DNA in frame 1.

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

Search for binding sites of a primer sequence within a template, with scientific mismatch tolerance. Uses position-dependent scoring (3' end weighted), nearest-neighbor thermodynamic Tm estimation, and configurable filtering. Finds both forward and reverse-complement binding sites.

Perform BLAST search on a DNA sequence

Export protein sequences translated from CDS in FASTA format


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned locus fxg01, find its coordinates without navigation, retrieve exactly that returned interval, then translate the retrieved DNA in frame 1.

Perform BLAST search on a DNA sequence


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] For pinned locus fxg01, find its coordinates without navigation, retrieve exactly that returned interval, then translate the retrieved DNA in frame 1.

[Tool] {"success":true,"sequence":"ATGGCTGAATTCCGTTAA","length":18,"chromosome":"px_core_A","start":401,"end":418,"strand":"+","format":"raw"}

Perform BLAST search on a DNA sequence


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Within the pinned interval on px_core_B, list matching CDS annotations and then fetch full details for the first locus tag returned.

List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

List current tasks in the workspace task tracking system, optionally filtered by status.

List all positional highlights currently shown for the active tab, including each highlight's id, chromosome, start/end coordinates (1-based inclusive), length, label, and color. Use this to review what is highlighted or to obtain an id before calling remove_highlight.

Analyze codon usage patterns in DNA coding sequence with comprehensive statistics and visualization. Supports analysis by direct sequence input, gene name, or locus tag.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Within the pinned interval on px_core_B, list matching CDS annotations and then fetch full details for the first locus tag returned.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt protein snapshot for synthetic protein record pcf004, retrieve the first returned accession with its sequence, and calculate that returned protein sequence's molecular weight. This is a UniProt lookup, not a genome-gene search.

Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.

Retrieve detailed information for a specific UniProt entry including sequence, annotations, functions, and cross-references.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.

Search PDB database for experimental protein structures by gene name. Returns available X-ray crystallography, NMR, cryo-EM, and other experimental structure data.

x-ray
nmr
cryo-em
neutron
fiber diffraction

Search for genomic features by ANNOTATION TEXT, FUNCTION KEYWORD, or FEATURE TYPE (e.g., find all tRNA, all kinase-related CDS, all transport proteins). This is a BROAD search across all feature types. Do NOT use this to look up a specific gene by its name — use find_gene_by_name or jump_to_gene instead.

Get protein annotations from UniProt


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt protein snapshot for synthetic protein record pcf004, retrieve the first returned accession with its sequence, and calculate that returned protein sequence's molecular weight. This is a UniProt lookup, not a genome-gene search.

[Tool] {"success":true,"results_count":1,"entries":[{"accession":"QX004A","protein_name":"Pinned catalytic family 004","gene_name":"pcf004","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}

Get protein annotations from UniProt


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt protein snapshot for synthetic protein record pcf004, retrieve the first returned accession with its sequence, and calculate that returned protein sequence's molecular weight. This is a UniProt lookup, not a genome-gene search.

[Tool] {"success":true,"results_count":1,"entries":[{"accession":"QX004A","protein_name":"Pinned catalytic family 004","gene_name":"pcf004","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}

[Tool] {"success":true,"entry_info":{"accession":"QX004A","protein_name":"Pinned catalytic family 004","gene_name":"pcf004","organism":"Synthetic bacterium Alpha","reviewed":true},"protein_sequence":"MEFGHIKLMNPQRSTVWYGAVLIPFYWST","sequence_length":29}

Get protein annotations from UniProt


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Find the synthetic gene synA17, then return exactly the DNA interval reported by that search result.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Search InterPro database for domain families, functional sites, and protein signatures using keywords, names, or descriptions. Enhanced with advanced filtering and batch processing capabilities.

Jump directly to a gene location by gene name or locus tag. This is the PRIMARY tool for navigating to genes when you know the gene name.

Search for specific sequence motifs or patterns within genomic regions. Supports exact matches, IUPAC ambiguity codes (N=any, R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=not A, D=not C, H=not G, V=not T), regular expressions, and mismatch tolerance.

Searches for a regular expression or nucleotide pattern across a specified genomic region.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Find the synthetic gene synA17, then return exactly the DNA interval reported by that search result.

[Tool] {"success":true,"genes_found":1,"genes":[{"name":"synA17","locus_tag":"synA017","chromosome":"fixture_contig_A","start":731,"end":760,"strand":"+"}]}

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] List CDS annotations in the pinned fixture interval, then retrieve full details for the first annotation returned by that list.

Display the Action List Manager interface for queued sequence-editing Actions. Actions are genome edit operations, not checklist Tasks.

Export coding sequences (CDS) in FASTA format

Delete a genome annotation by identifier (locus_tag, gene name, or protein_id) with change tracking. Use this when the user explicitly asks to delete or remove a specific annotation. NOT the same as delete_sequence which removes sequence data.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] List CDS annotations in the pinned fixture interval, then retrieve full details for the first annotation returned by that list.

List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

List all positional highlights currently shown for the active tab, including each highlight's id, chromosome, start/end coordinates (1-based inclusive), length, label, and color. Use this to review what is highlighted or to obtain an id before calling remove_highlight.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Read bases 101 through 112 from fixture_contig_A, then reverse-complement the sequence returned by that read.

Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).

Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.

Export sequences in FASTA format


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Read bases 101 through 112 from fixture_contig_A, then reverse-complement the sequence returned by that read.

[Tool] {"success":true,"sequence":"ATGCCGTTAACG","length":12,"chromosome":"fixture_contig_A","start":101,"end":112,"strand":"+","format":"raw"}

Export sequences in FASTA format


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the coding fragment at fixture_contig_A positions 301 to 315, then translate the DNA returned by that retrieval in frame 1.

Create BLAST protein database from loaded genome using 6-frame translation

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

Analyze codon usage patterns in DNA coding sequence with comprehensive statistics and visualization. Supports analysis by direct sequence input, gene name, or locus tag.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the coding fragment at fixture_contig_A positions 301 to 315, then translate the DNA returned by that retrieval in frame 1.

[Tool] {"success":true,"sequence":"ATGGCTGAACTGTAA","length":15,"chromosome":"fixture_contig_A","start":301,"end":315,"strand":"+","format":"raw"}

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt snapshot for reviewed bacterial ribosomal protein L35 entries, then retrieve the first accession returned by the search with its sequence.

Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.

Retrieve detailed information for a specific UniProt entry including sequence, annotations, functions, and cross-references.

Get detailed protein information from UniProt

Perform BLAST sequence similarity search using NCBI online databases

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt snapshot for reviewed bacterial ribosomal protein L35 entries, then retrieve the first accession returned by the search with its sequence.

[Tool] {"success":true,"results_count":1,"entries":[{"accession":"P0A7E1","protein_name":"50S ribosomal protein L35","gene_name":"rpmI","organism":"Escherichia coli","reviewed":true}]}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Analyze domains in this protein sequence

Analyze protein domains, families, and functional sites using InterPro database. Provides comprehensive domain architecture, functional annotations, and evolutionary relationships.

Perform BLAST search on a protein sequence

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.

Detect whether a sequence is DNA, RNA, or protein

Open an interactive 3D protein structure viewer from cached data, a local PDB file, an online PDB URL, a UniProt/AlphaFold accession, a PDB ID, or a gene name. Online structures are downloaded automatically.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Create a BLAST database from the loaded chromosome

Create BLAST nucleotide database from a specific chromosome of the currently loaded genome. Use this ONLY when you want to index a single chromosome and have its exact name from the loaded genome (e.g. U00096, NC_000913.3). Do not use this for the entire genome.

List all available BLAST databases (online, local, and custom)

Create a new BLAST database from FASTA file for local searches

Delete a local BLAST database

Quickly create BLAST databases (both nucleotide and protein) for the entire currently loaded genome. Use this as the default/quick way to index the genome when no specific chromosome name is specified. Automatically associates databases with the genome for smart database selection.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Make a searchable database for E. coli K-12 genome

Validate a local BLAST database integrity and format

Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.

Create BLAST protein database from loaded genome using 6-frame translation

Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search this DNA sequence against NCBI nucleotide database

Perform BLAST search on a DNA sequence

Perform BLAST sequence similarity search against various databases. Supports nucleotide and protein sequences with comprehensive search options.

Search for specific sequence motifs or patterns within genomic regions. Supports exact matches, IUPAC ambiguity codes (N=any, R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=not A, D=not C, H=not G, V=not T), regular expressions, and mismatch tolerance.

Search InterPro database for domain families, functional sites, and protein signatures using keywords, names, or descriptions. Enhanced with advanced filtering and batch processing capabilities.

Run BLAST on a sequence extracted directly from a loaded genome chromosome region.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] BLAST this protein sequence against SwissProt

Perform BLAST sequence similarity search using NCBI online databases


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Hide the gene track

Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.

genes gc_content sequence variants reads proteins primers actions wigTracks blast

Show, hide, or toggle the main ChatBox panel. Use this for the ChatBox itself, not the ChatBox settings modal.

Expand, collapse, or toggle the main genome browser Sidebar while keeping its toolbar and splitter controls synchronized.

Set settings for a specific track type in the genome browser (genes, primers, reads, sequence, gc, variants, actions, blast, wigTracks, sequenceLine). Only provided parameters will be updated. For multi-instance tracks, provide file_id to update instance-specific settings.

genes primers reads sequence gc variants actions blast wigTracks sequenceLine

Open or close application settings modals/panels. Use this when users ask to open, close, show, hide, or toggle any settings interface such as LLM configuration, ChatBox settings, General settings, Track settings, MCP server settings, Multi-Agent settings, etc.

Get the current visibility status of all tracks in the genome browser. Returns which tracks (genes, sequence, gc, variants, reads, proteins) are currently visible and their descriptions. Use this when the user asks about track visibility, which tracks are shown/hidden, or current track status. NOT the same as get_all_track_settings which returns detailed configuration/settings for each track.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Show GC content

Calculate GC content for a chromosome coordinate range from the currently loaded genome. Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.

Get current settings for a specific track type in the genome browser (genes, primers, reads, sequence, gc, variants, actions, blast, wigTracks, sequenceLine). For multi-instance tracks, provide file_id to get instance-specific settings.

Save a named genomic position or region bookmark for quick navigation later. Use this when the user asks to bookmark, pin, flag, or save a specific coordinate range. This stores only the genomic interval, not track visibility or full workspace layout.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Attach the note curated independently to the annotation identified as geneX.

Legacy compatibility tool that creates a reviewable annotation ChangeSet; it does not mutate an annotation directly.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Create a new user-defined annotation

gene CDS mRNA tRNA rRNA promoter regulatory terminator ribosome_binding_site primer other

Export sequence or annotation data

Delete a genome annotation by identifier (locus_tag, gene name, or protein_id) with change tracking. Use this when the user explicitly asks to delete or remove a specific annotation. NOT the same as delete_sequence which removes sequence data.

Save a primer oligo to the primer library (stored separately from the genome, never written into the genome file). Binding sites are predicted automatically; provide chromosome/start/end only to pin a specific manual placement.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Attach the note curated independently to the annotation identified as geneX.

Create a new user-defined annotation

Export sequence or annotation data


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Show at most ten edit-history entries for annotation geneX.

Retrieve change history for a specific annotation or the entire genome

Rank gene-associated annotation features for curation using deterministic quality signals. Covers CDS, gene, mRNA, coding and non-coding RNA types, collapses co-located duplicate records, and prefers CDS at a shared locus.

include exclude-active exclude-completed exclude-covered

List the durable, per-genome Deep Gene Research history used to prevent repeated annotation research across agents and automation runs.

active completed completed_unarchived failed cancelled

Privileged raw structural editing of one existing genome annotation. Requires authenticated MCP permission annotation:structural and bypasses the qualifier-only ChangeSet workflow.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, find gene fxg01 exactly (do not navigate the view), then retrieve the sequence of exactly the returned interval.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.

Get the list of all chromosomes (contigs/scaffolds) in the currently loaded genome, including their names, lengths, and which one is currently selected. Use this when the user asks about chromosome names, genome contigs, scaffold list, or wants to know what chromosomes are available.

Get status of a specific agent


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, find gene fxg01 exactly (do not navigate the view), then retrieve the sequence of exactly the returned interval.

Get status of a specific agent


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-548, then compute the GC content of that retrieved sequence.

Get the complete schema of available settings for all track types

Get the current status of the benchmark system, including initialization state, whether a benchmark is currently running or paused, and how many test suites are loaded.

Get detailed information about a specific DNA marker/ladder, including all band sizes, recommended gel percentage, and description.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-548, then compute the GC content of that retrieved sequence.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAAGCTACACGAGTA","length":49,"chromosome":"px_core_A","start":500,"end":548,"strand":"+","format":"raw"}

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-542, then return the reverse complement of that retrieved sequence.

Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).

Get the current visibility status of all tracks in the genome browser. Returns which tracks (genes, sequence, gc, variants, reads, proteins) are currently visible and their descriptions. Use this when the user asks about track visibility, which tracks are shown/hidden, or current track status. NOT the same as get_all_track_settings which returns detailed configuration/settings for each track.

Get predicted operon structures for a chromosome from loaded annotations. Returns operon coordinates, strand, gene count, member genes, and length. Use this when the user asks to show, list, find, predict, or inspect operons in the current genome.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-542, then return the reverse complement of that retrieved sequence.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAAGCTACA","length":43,"chromosome":"px_core_A","start":500,"end":542,"strand":"+","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-536, then calculate the molecular weight of that retrieved sequence.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.

Get the benchmark results history. Returns statistics from all previous benchmark runs, including success rates, test counts, durations, and the latest run details.

Get current settings for all track types in the genome browser


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-536, then calculate the molecular weight of that retrieved sequence.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAA","length":37,"chromosome":"px_core_A","start":500,"end":536,"strand":"+","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，查找 BamHI 酶切位点，然后对整段序列做虚拟酶切。

Locates recognition and cleavage sites for restriction endonucleases in a genomic region. Supports 80+ enzymes with IUPAC ambiguity codes, staggered cut positions (5' overhang, 3' overhang, blunt end), and HF variants.

Performs an in-silico restriction digest of a chromosome or sequence using one or more restriction enzymes. Calculates fragment positions, sizes, end types (5' overhang, 3' overhang, blunt), and provides digest map for gel electrophoresis visualization.

Search for binding sites of a primer sequence within a template, with scientific mismatch tolerance. Uses position-dependent scoring (3' end weighted), nearest-neighbor thermodynamic Tm estimation, and configurable filtering. Finds both forward and reverse-complement binding sites.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，查找 BamHI 酶切位点，然后对整段序列做虚拟酶切。

[Tool] {"success":true,"sequence":"TCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":43,"chromosome":"px_core_B","start":500,"end":542,"strand":"-","format":"raw"}

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，查找 BamHI 酶切位点，然后对整段序列做虚拟酶切。

[Tool] {"success":true,"sequence":"TCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":43,"chromosome":"px_core_B","start":500,"end":542,"strand":"-","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, list the annotations on px_core_A, then fetch the full details of the first listed annotation.

List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Retrieve a resumable DGR research workflow; annotation:propose callers materialize completed proposals as reviewable ChangeSets, while research-only callers can defer that step.

Rank gene-associated annotation features for curation using deterministic quality signals. Covers CDS, gene, mRNA, coding and non-coding RNA types, collapses co-located duplicate records, and prefers CDS at a shared locus.

List lightweight annotation ChangeSet summaries for single or batch human review.

List the durable, per-genome Deep Gene Research history used to prevent repeated annotation research across agents and automation runs.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, list the annotations on px_core_A, then fetch the full details of the first listed annotation.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，查看 px_core_B:525 附近 5000bp 内的特征，并取出第一个特征的完整注释。

Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position, genes around a location, or what is nearby a genomic coordinate. NOT the same as navigate_to_position which moves the view, or list_annotations which lists all annotations in a region.

Retrieve an annotation ChangeSet and its validation, approval, or commit state.

Retrieve change history for a specific annotation or the entire genome

Get the per-genome revisioned annotation ChangeSet audit trail.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，查看 px_core_B:525 附近 5000bp 内的特征，并取出第一个特征的完整注释。


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In the pinned UniProt fixture corpus, search for "pinned catalytic", then fetch the full entry of the first search result.

Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.

Retrieve detailed information for a specific UniProt entry including sequence, annotations, functions, and cross-references.

Retrieve detailed information for a specific InterPro entry including description, member databases, protein matches, and structural data.

Search InterPro database for domain families, functional sites, and protein signatures using keywords, names, or descriptions. Enhanced with advanced filtering and batch processing capabilities.

Searches for a regular expression or nucleotide pattern across a specified genomic region.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In the pinned UniProt fixture corpus, search for "pinned catalytic", then fetch the full entry of the first search result.

[Tool] {"success":true,"results_count":5,"entries":[{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}