[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 corpus for a catalytic protein, fetch the first entry, then run a domain analysis on that entry.

[Tool] {"success":true,"results_count":3,"entries":[{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}


[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 corpus for a catalytic protein, fetch the first entry, then run a domain analysis on that entry.

[Tool] {"success":true,"results_count":3,"entries":[{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}

[Tool] {"success":true,"entry_info":{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true},"protein_sequence":"MACDEFGHIKLMNPQRSTVWYGAVLIPFY","sequence_length":29}

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

experimental homology predicted uncertain

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.

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

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

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

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] 将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。

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

Create a new BLAST database from FASTA file for local searches

Validate a local BLAST database integrity and format

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

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.

Delete a local BLAST database


[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] 将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

Delete a local BLAST database


[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] 将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

[Tool] {"success":true,"database":{"name":"px_nucl","type":"nucleotide"},"dbName":"px_nucl"}

Delete a local BLAST database


[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] 将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

[Tool] {"success":true,"database":{"name":"px_nucl","type":"nucleotide"},"dbName":"px_nucl"}

[Tool] {"success":true,"valid":true,"database":"px_nucl"}

Delete a local BLAST database


[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 fxg17 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.

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.

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

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

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] In pinned synthetic sample PX-01, find gene fxg17 exactly (do not navigate the view), then retrieve the sequence of exactly the returned 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] 在只读夹具 PX-01 中，精确查找基因 fxg18（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。

Get list of all currently loaded files in the genome browser with their complete paths 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] 在只读夹具 PX-01 中，精确查找基因 fxg18（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。


[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，精确查找基因 fxg18（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。


[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 compute the GC content of that retrieved sequence.

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

Get status of a specific agent

Get current settings for all track types in the genome browser

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


[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 compute the GC content of that retrieved sequence.

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

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] 在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，并计算该序列的熵。

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.

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

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 the complete schema of available settings for all track types


[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，并计算该序列的熵。

[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, retrieve the + strand of px_core_A:500-542, 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.

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


[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 calculate the molecular weight 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] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 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.

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] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 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":"CGGAATTCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":49,"chromosome":"px_core_B","start":500,"end":548,"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.

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] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 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":"CGGAATTCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":49,"chromosome":"px_core_B","start":500,"end":548,"strand":"-","format":"raw"}

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, 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.

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

Get the per-genome revisioned annotation ChangeSet audit trail.

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


[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。

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

Retrieve change history for a specific annotation or the entire 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] 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.

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

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


[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，精确查找基因 fxg08（不要跳转视图），取出其返回区间的序列，并计算该序列的 GC 含量。

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.

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 complete schema of available settings for all track types


[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，精确查找基因 fxg08（不要跳转视图），取出其返回区间的序列，并计算该序列的 GC 含量。

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，精确查找基因 fxg08（不要跳转视图），取出其返回区间的序列，并计算该序列的 GC 含量。

[Tool] {"success":true,"sequence":"TTAAGCGTCGGTCAGTTTATACAT","length":24,"chromosome":"px_core_B","start":3838,"end":3861,"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] 先列出已加载浏览器中所有轨道的可见性，然后打开蛋白质轨道。

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.

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

Get current settings for all track types in the genome browser

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.

genes primers reads sequence gc variants actions blast wigTracks sequenceLine

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.


[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] 先列出已加载浏览器中所有轨道的可见性，然后打开蛋白质轨道。


[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] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

Remove all tasks from the workspace task tracking system.

Add a new task to the workspace tasks list for tracking progress during complex operations.

Update the status, title, or progress of an existing task in the tasks list.

Delete a task from the workspace tasks list.

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

all pending in_progress completed failed

Legacy compatibility tool that creates a reviewable annotation ChangeSet; it does not mutate an annotation 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] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

[Tool] {"success":true,"cleared":1}


[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] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}


[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] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}

[Tool] {"success":true,"updated":1,"task_id":"task_763"}


[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] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}

[Tool] {"success":true,"updated":1,"task_id":"task_763"}

[Tool] {"success":true,"deleted":1,"task_id":"task_763"}


[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 regulatory annotation named px_reg_A on U00096 at 200000-200600, update its note to 'px conserved region', then fetch its change history.

Create a new user-defined annotation

gene CDS mRNA tRNA rRNA promoter regulatory terminator ribosome_binding_site primer other

Retrieve change history for a specific annotation or the entire genome

Get the per-genome revisioned annotation ChangeSet audit trail.

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.

Validate structured research evidence and create a reviewable annotation ChangeSet without modifying the 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] Create a regulatory annotation named px_reg_A on U00096 at 200000-200600, update its note to 'px conserved region', then fetch its change history.

[Tool] {"success":true,"annotation_id":"user_60_365f73","id":"user_60_365f73","identifier":"user_60_365f73","chromosome":"U00096","start":200000,"end":200600,"type":"regulatory","name":"px_reg_A"}

Create a new user-defined 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] Create a regulatory annotation named px_reg_A on U00096 at 200000-200600, update its note to 'px conserved region', then fetch its change history.

[Tool] {"success":true,"annotation_id":"user_60_365f73","id":"user_60_365f73","identifier":"user_60_365f73","chromosome":"U00096","start":200000,"end":200600,"type":"regulatory","name":"px_reg_A"}

[Tool] {"success":true,"updated":1,"deleted":1,"cleared":1}

Create a new user-defined 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] 在固定 UniProt 语料中搜索催化蛋白，获取第一条条目，然后对该条目进行结构域分析。

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.

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

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

Retrieve detailed information for a specific InterPro entry including description, member databases, protein matches, and structural 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] 在固定 UniProt 语料中搜索催化蛋白，获取第一条条目，然后对该条目进行结构域分析。

[Tool] {"success":true,"results_count":3,"entries":[{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}


[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] 在固定 UniProt 语料中搜索催化蛋白，获取第一条条目，然后对该条目进行结构域分析。

[Tool] {"success":true,"results_count":3,"entries":[{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}

[Tool] {"success":true,"entry_info":{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true},"protein_sequence":"MACDEFGHIKLMNPQRSTVWYGAVLIPFY","sequence_length":29}


[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] Export the current view to /tmp/px_blast.fasta, build a nucleotide database named px_nucl from it, validate the database, then list all databases.

Export sequences from the current genome view in FASTA format

Create a new BLAST database from FASTA file for local searches

Validate a local BLAST database integrity and format

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

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.

Delete a local BLAST database


[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] Export the current view to /tmp/px_blast.fasta, build a nucleotide database named px_nucl from it, validate the database, then list all databases.

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

Delete a local BLAST database


[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] Export the current view to /tmp/px_blast.fasta, build a nucleotide database named px_nucl from it, validate the database, then list all databases.

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

[Tool] {"success":true,"database":{"name":"px_nucl","type":"nucleotide"},"dbName":"px_nucl"}

Delete a local BLAST database


[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] Export the current view to /tmp/px_blast.fasta, build a nucleotide database named px_nucl from it, validate the database, then list all databases.

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

[Tool] {"success":true,"database":{"name":"px_nucl","type":"nucleotide"},"dbName":"px_nucl"}

[Tool] {"success":true,"valid":true,"database":"px_nucl"}

Delete a local BLAST database


[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，精确查找基因 fxg16（不要跳转视图），然后取出其返回区间的序列。

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 status of a specific agent

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] 在只读夹具 PX-01 中，精确查找基因 fxg16（不要跳转视图），然后取出其返回区间的序列。

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 fxg17 exactly (do not navigate the view), fetch its gene details, then retrieve the sequence of exactly the returned interval.

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, find gene fxg17 exactly (do not navigate the view), fetch its gene details, then retrieve the sequence of exactly the returned 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] In pinned synthetic sample PX-01, find gene fxg17 exactly (do not navigate the view), fetch its gene details, then retrieve the sequence of exactly the returned 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] 在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，并计算该序列的 GC 含量。

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

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 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.


[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，并计算该序列的 GC 含量。

[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, retrieve the + strand of px_core_A:500-548, then compute the entropy of that retrieved 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.

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

Get the current sequence-editing Action queue. Actions are queued genome edit operations, not checklist Tasks.

Get current status of a workflow execution


[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 entropy of that retrieved sequence.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAAGCTACACGAGTA","length":49,"chromosome":"px_core_A","start":500,"end":548,"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:500-536 - 链的序列，并返回它的反向互补序列。

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

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.

Get list of available functions for a plugin

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] 在只读夹具 PX-01 中，取出 px_core_B:500-536 - 链的序列，并返回它的反向互补序列。

[Tool] {"success":true,"sequence":"AACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":37,"chromosome":"px_core_B","start":500,"end":536,"strand":"-","format":"raw"}

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:500-542, then translate that retrieved DNA in reading frame 2.

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 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] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-542, then translate that retrieved DNA in reading frame 2.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAAGCTACA","length":43,"chromosome":"px_core_A","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:500-548 - 链的序列，并计算其分子量。

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 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 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] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并计算其分子量。

[Tool] {"success":true,"sequence":"CGGAATTCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":49,"chromosome":"px_core_B","start":500,"end":548,"strand":"-","format":"raw"}

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:500-536, find EcoRI restriction sites in that retrieved sequence, then run a virtual digest of the full sequence.

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.

Retrieve change history for a specific annotation or the entire 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:500-536, find EcoRI restriction sites in that retrieved sequence, then run a virtual digest of the full 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] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-536, find EcoRI restriction sites in that retrieved sequence, then run a virtual digest of the full 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] In pinned synthetic sample PX-01, find features near px_core_A:525 within 5000 bp, then fetch the full annotation of the first feature.

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

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


[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 features near px_core_A:525 within 5000 bp, then fetch the full annotation of the first feature.


[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] 在只读夹具的 UniProt 语料中搜索 "pinned catalytic"，并取出第一条结果条目的完整信息。

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.

Get list of available functions for a plugin

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.


[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] 在只读夹具的 UniProt 语料中搜索 "pinned catalytic"，并取出第一条结果条目的完整信息。

[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}]}


[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 fxg07 exactly (do not navigate the view), retrieve the sequence of exactly the returned interval, then compute the GC content of that 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.

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.

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

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.

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

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] In pinned synthetic sample PX-01, find gene fxg07 exactly (do not navigate the view), retrieve the sequence of exactly the returned interval, then compute the GC content of that 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, find gene fxg07 exactly (do not navigate the view), retrieve the sequence of exactly the returned interval, then compute the GC content of that sequence.

[Tool] {"success":true,"sequence":"ATGCAATATAAACTGACCTAA","length":21,"chromosome":"px_core_A","start":3701,"end":3721,"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:500-548 - 链的序列，按阅读框 3 翻译，并计算所得蛋白的分子量。

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

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. 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 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] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，按阅读框 3 翻译，并计算所得蛋白的分子量。

[Tool] {"success":true,"sequence":"CGGAATTCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":49,"chromosome":"px_core_B","start":500,"end":548,"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:500-548 - 链的序列，按阅读框 3 翻译，并计算所得蛋白的分子量。

[Tool] {"success":true,"sequence":"CGGAATTCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":49,"chromosome":"px_core_B","start":500,"end":548,"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 the loaded genome browser, list the visibility of all tracks first, then open the proteins 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.

Get the complete schema of available settings for all track types

Get current settings for all track types in the genome browser

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.

Get current status of a workflow execution


[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 loaded genome browser, list the visibility of all tracks first, then open the proteins 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] 关闭基因组浏览器中的读段轨道，然后重新检查当前轨道可见性。

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] 关闭基因组浏览器中的读段轨道，然后重新检查当前轨道可见性。

[Tool] {"success":true,"track":"reads","visible":false}

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] Clear the pending task list, create a task named PX-verify with status in_progress and progress 25, mark it completed with progress 100, delete it, then list all tasks to confirm.

Remove all tasks from the workspace task tracking system.

Add a new task to the workspace tasks list for tracking progress during complex operations.

Update the status, title, or progress of an existing task in the tasks list.

Delete a task from the workspace tasks list.

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

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] Clear the pending task list, create a task named PX-verify with status in_progress and progress 25, mark it completed with progress 100, delete it, then list all tasks to confirm.

[Tool] {"success":true,"cleared":1}


[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] Clear the pending task list, create a task named PX-verify with status in_progress and progress 25, mark it completed with progress 100, delete it, then list all tasks to confirm.

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}


[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] Clear the pending task list, create a task named PX-verify with status in_progress and progress 25, mark it completed with progress 100, delete it, then list all tasks to confirm.

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}

[Tool] {"success":true,"updated":1,"task_id":"task_763"}


[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] Clear the pending task list, create a task named PX-verify with status in_progress and progress 25, mark it completed with progress 100, delete it, then list all tasks to confirm.

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}

[Tool] {"success":true,"updated":1,"task_id":"task_763"}

[Tool] {"success":true,"deleted":1,"task_id":"task_763"}


[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 U00096 上创建名为 px_reg_A 的调控注释（200000-200600），将其 note 更新为 px conserved region，然后获取它的变更历史。

Create a new user-defined annotation

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

Retrieve change history for a specific annotation or the entire genome

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

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

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] 在 U00096 上创建名为 px_reg_A 的调控注释（200000-200600），将其 note 更新为 px conserved region，然后获取它的变更历史。

[Tool] {"success":true,"annotation_id":"user_60_365f73","id":"user_60_365f73","identifier":"user_60_365f73","chromosome":"U00096","start":200000,"end":200600,"type":"regulatory","name":"px_reg_A"}

Create a new user-defined 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 U00096 上创建名为 px_reg_A 的调控注释（200000-200600），将其 note 更新为 px conserved region，然后获取它的变更历史。

[Tool] {"success":true,"annotation_id":"user_60_365f73","id":"user_60_365f73","identifier":"user_60_365f73","chromosome":"U00096","start":200000,"end":200600,"type":"regulatory","name":"px_reg_A"}

[Tool] {"success":true,"updated":1,"deleted":1,"cleared":1}

Create a new user-defined 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] Search the pinned UniProt corpus for a catalytic protein, fetch the first entry, then run a domain analysis on that entry.

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.

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

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

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

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


[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 corpus for a catalytic protein, fetch the first entry, then run a domain analysis on that entry.

[Tool] {"success":true,"results_count":3,"entries":[{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}


[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 corpus for a catalytic protein, fetch the first entry, then run a domain analysis on that entry.

[Tool] {"success":true,"results_count":3,"entries":[{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}

[Tool] {"success":true,"entry_info":{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true},"protein_sequence":"MACDEFGHIKLMNPQRSTVWYGAVLIPFY","sequence_length":29}


[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] 将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。

Export sequences from the current genome view in FASTA format

Create a new BLAST database from FASTA file for local searches

Validate a local BLAST database integrity and format

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

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] 将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

Delete a local BLAST database


[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] 将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

[Tool] {"success":true,"database":{"name":"px_nucl","type":"nucleotide"},"dbName":"px_nucl"}

Delete a local BLAST database


[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] 将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。

[Tool] {"success":true,"exported":1,"filePath":"/tmp/px_blast.fasta"}

[Tool] {"success":true,"database":{"name":"px_nucl","type":"nucleotide"},"dbName":"px_nucl"}

[Tool] {"success":true,"valid":true,"database":"px_nucl"}

Delete a local BLAST database


[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 fxg15 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 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.

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] In pinned synthetic sample PX-01, find gene fxg15 exactly (do not navigate the view), then retrieve the sequence of exactly the returned interval.