[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-41 里精确查找人工基因 fxg01，不要跳转当前视图。

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.

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.

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

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

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

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] 核对 PX-72：列出 px_core_B:6007-6099 内的 CDS 注释，最多 7 条。

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.

Retrieve change history for a specific annotation or the entire genome

Export protein sequences translated from CDS in FASTA format

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

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.

Export coding sequences (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] 请从 undefined 的固定数据中取回 px003 的完整注释记录（样本 PX-103）。

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.

Create a new user-defined annotation

gene CDS mRNA tRNA rRNA promoter regulatory terminator ribosome_binding_site primer other

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.

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] 为固定寡核苷酸 PX-196 生成反向互补序列，并校验碱基：CGTCCCAGGTATTGTTTCCCGCTCCTTGTG。

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 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.

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.


[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] 使用 standard 密码表和第 1 阅读框翻译样本 PX-227：ATGTATAAACTGACCGACGCTTAA；保留终止符。

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

standard vertebrate_mitochondrial bacterial archaeal

Load annotation files (GFF/BED/GTF) 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] Run the GC quality metric for pinned sequence PX-249, with case normalization enabled: TTTCGGGAGACGCTTGCCCAACCCCGTAT.

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

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

Detect whether a sequence is DNA, RNA, or protein

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.

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.

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] Run the GC quality metric for pinned sequence PX-250, with case normalization enabled: TCTTCTCAGTCGCGGCCGGAGAGAACCCTC.

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.

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.

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.


[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] Run the GC quality metric for pinned sequence PX-251, with case normalization enabled: CGCCGAGATGCTAATTCTTCACAACCTCAGG.

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] Run the GC quality metric for pinned sequence PX-252, with case normalization enabled: CAAGCTGGAAGAGACCGCGATCCCCGCATTGG.

Perform BLAST search on a DNA sequence

Cut a sequence region into the sequence-editing clipboard and queue a cut Action. This is not a checklist Task. Use paste_sequence after this to queue a move, and 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] Run the GC quality metric for pinned sequence PX-253, with case normalization enabled: CACGGTAATAGACCAGTTAGGCAA.

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] Run the GC quality metric for pinned sequence PX-254, with case normalization enabled: GGAAGGTTCTCCATACGTGGACGTT.


[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] Run the GC quality metric for pinned sequence PX-255, with case normalization enabled: TCAGTATCCGAACGTATCGTTAAACC.

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] Run the GC quality metric for pinned sequence PX-256, with case normalization enabled: GGGGAGGACTGATATTGGCGATCAAAG.


[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] 计算固定序列 PX-258 的 GC 比例，启用大小写归一化：GGCCGGTATAAATCTGTTGGGGGGCGACC。

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] 求合成序列 PX-289 的 Shannon 复杂度：TCTTGGGTACGCCGCCGATTTCGG。

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.

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

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.

Predict promoter regions in 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] 按 protein 类型计算固定样本 PX-320 的分子量：MLMNPQRSTVWYGAVLIPFYWST。

Get detailed protein information from UniProt

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

experimental homology predicted uncertain

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

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

Detect whether a sequence is DNA, RNA, or protein


[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] 分析合成实验 PX-351 的引物长度、GC、Tm 和发卡风险：CGCTGGGACGGTATTACC。

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.

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.

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.

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.

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.


[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.

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.

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.

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.

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

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] 在冻结的 UniProt 蛋白快照中检索 Synthetic archaeon Gamma 的人工蛋白记录 pcf006，最多返回 4 条（PX-506）；这是 UniProt 检索，不是基因组基因查找。

Search UniProt database for protein information

Get protein annotations from UniProt

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

Advanced UniProt search with multiple query fields, filters, and complex search criteria. Supports boolean operators and field-specific searches.


[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] 取回固定蛋白条目 QX017A 及其氨基酸序列，核对编号 PX-537。

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

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.

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] 在冻结基因组中只读查找人工位点 fxg11；把检索结果里的染色体和边界用于取序列，再将返回的 DNA 按第一阅读框翻译。

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

Predict promoter regions in 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.


[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] 在冻结基因组中只读查找人工位点 fxg11；把检索结果里的染色体和边界用于取序列，再将返回的 DNA 按第一阅读框翻译。

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] 在冻结基因组中只读查找人工位点 fxg11；把检索结果里的染色体和边界用于取序列，再将返回的 DNA 按第一阅读框翻译。

[Tool] {"success":true,"sequence":"ATGACCGACGCTGAATAA","length":18,"chromosome":"px_core_A","start":5901,"end":5918,"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] 先在 px_core_B 的固定区间 8213-8280 内列出 tRNA 注释，再用列表返回的第一个 locus tag 获取完整详情。

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 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.

Update multiple annotations in a single operation with change tracking

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] 先在 px_core_B 的固定区间 8213-8280 内列出 tRNA 注释，再用列表返回的第一个 locus tag 获取完整详情。

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.

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] 在冻结的 UniProt 蛋白快照中检索 Synthetic archaeon Gamma 的人工蛋白记录 pcf012，用首条结果的 accession 获取蛋白序列，然后计算该返回序列的蛋白分子量；这是 UniProt 检索，不是基因组基因查找。

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

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 UniProt database for protein information


[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] 在冻结的 UniProt 蛋白快照中检索 Synthetic archaeon Gamma 的人工蛋白记录 pcf012，用首条结果的 accession 获取蛋白序列，然后计算该返回序列的蛋白分子量；这是 UniProt 检索，不是基因组基因查找。

[Tool] {"success":true,"results_count":1,"entries":[{"accession":"QX012A","protein_name":"Pinned catalytic family 012","gene_name":"pcf012","organism":"Synthetic archaeon Gamma","reviewed":false,"length":31}]}

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

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


[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] 在冻结的 UniProt 蛋白快照中检索 Synthetic archaeon Gamma 的人工蛋白记录 pcf012，用首条结果的 accession 获取蛋白序列，然后计算该返回序列的蛋白分子量；这是 UniProt 检索，不是基因组基因查找。

[Tool] {"success":true,"results_count":1,"entries":[{"accession":"QX012A","protein_name":"Pinned catalytic family 012","gene_name":"pcf012","organism":"Synthetic archaeon Gamma","reviewed":false,"length":31}]}

[Tool] {"success":true,"entry_info":{"accession":"QX012A","protein_name":"Pinned catalytic family 012","gene_name":"pcf012","organism":"Synthetic archaeon Gamma","reviewed":false},"protein_sequence":"MCDEFGHIKLMNPQRSTVWYGAVLIPFYWST","sequence_length":31}


[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] High-stringency protein search with BLOSUM80

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

Search AlphaFold database for protein structures

⚠ 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.

Perform BLAST search on a protein sequence