[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill-google-deepmind-ncbi-sequence-fetch":3,"mdc-3ts9r5-key":36,"related-org-google-deepmind-ncbi-sequence-fetch":2031,"related-repo-google-deepmind-ncbi-sequence-fetch":2193},{"slug":4,"name":4,"fn":5,"description":6,"org":7,"tags":11,"stars":25,"repoUrl":26,"updatedAt":27,"license":28,"forks":29,"topics":30,"repo":31,"sourceUrl":34,"mdContent":35},"ncbi-sequence-fetch","retrieve sequences from NCBI databases","Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},"google-deepmind","Google DeepMind","https:\u002F\u002Fpexgzepcugksgbtrxkhf.supabase.co\u002Fstorage\u002Fv1\u002Fobject\u002Fpublic\u002Forg-logos\u002Fgoogle-deepmind.png",[12,16,19,22],{"name":13,"slug":14,"type":15},"Research","research","tag",{"name":17,"slug":18,"type":15},"Bioinformatics","bioinformatics",{"name":20,"slug":21,"type":15},"NCBI","ncbi",{"name":23,"slug":24,"type":15},"Genomics","genomics",2333,"https:\u002F\u002Fgithub.com\u002Fgoogle-deepmind\u002Fscience-skills","2026-07-12T07:51:46.693436",null,234,[],{"repoUrl":26,"stars":25,"forks":29,"topics":32,"description":33},[],"GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other databases and tools.","https:\u002F\u002Fgithub.com\u002Fgoogle-deepmind\u002Fscience-skills\u002Ftree\u002FHEAD\u002Fskills\u002Fncbi_sequence_fetch","---\nname: ncbi-sequence-fetch\ndescription: >\n  Retrieve protein and nucleotide sequences from NCBI databases using\n  E-utilities. Supports direct accession lookup, CDS translation, gene+organism\n  search, locus lookup, PubMed-linked sequences, patent protein extraction, and\n  organism+length fallback search. Use when you need to fetch biological\n  sequences by accession, gene name, locus tag, PubMed ID, or patent number.\n---\n\n# NCBI Sequence Fetch\n\n## Prerequisites\n\n1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure\n    `uv` is installed and on PATH.\n2.  **User Notification**: If .licenses\u002Fncbi_sequence_fetch_LICENSE.txt does not\n    already exist in the workspace root directory then (1) prominently notify\n    the user to check the terms at https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002F and\n    https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Fhome\u002Fabout\u002Fpolicies\u002F, then (2) create the file\n    recording the notification text and timestamp.\n3.  **`.env` file**: Make sure the `.env` file exists in your home directory.\n    Create one if it does not exist.\n4.  **`NCBI_API_KEY`** (optional): Raises the NCBI rate limit from 3 to 10\n    requests\u002Fsecond. The skill works without it, but a key is recommended if the\n    user plans many queries or encounters a 429 error. You can register for a\n    key for free at https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Faccount\u002Fsettings\u002F. You **MUST**\n    use the safe credentials protocol in the `credentials` skill to check for\n    and request this key if this skill looks relevant to the user's request.\n\n## Core Rules\n\n-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the\n    database rather than accessing the database directly. The scripts\n    automatically enforce the required rate limit gracefully.\n-   **API Key Support**: If the user provides an `NCBI_API_KEY` in their\n    environment, the query speed limits are automatically increased\n    significantly.\n-   **Notification**: If this skill is used, ensure this is mentioned in the\n    output.\n\n## Overview\n\nWraps NCBI's Entrez E-utilities (efetch, esearch, elink, esummary) for\nretrieving protein and nucleotide sequences. Provides 10 subcommands covering\nthe full range of sequence retrieval workflows:\n\n-   `fetch-protein` — Direct protein accession lookup (GenPept, RefSeq)\n-   `fetch-nucleotide` — Direct nucleotide accession lookup\n-   `cds-translate` — Fetch CDS and translate to protein (3 methods)\n-   `search` — Free-text search of any NCBI database\n-   `elink` — Follow cross-database links (PubMed→Protein, etc.)\n-   `gene-protein` — Search protein by gene name + organism\n-   `locus-protein` — Search protein by locus tag + organism\n-   `pubmed-proteins` — Find proteins linked to a PubMed article\n-   `patent-search` — Extract protein sequences from patents\n-   `organism-length` — Last-resort search by organism + exact AA length\n\n## Utility Scripts\n\n**`scripts\u002Fncbi_fetch.py`** — Single script with subcommands.\n\nAll subcommands write structured JSON output. Use `--output FILE` to save to a\nfile, or omit it to print to stdout. A human-readable summary is always printed\nto stdout.\n\n### 1. Fetch Protein by Accession\n\nFetches protein FASTA from NCBI by accession (XP_, NP_, GenPept, etc.)\n\n```bash\nuv run scripts\u002Fncbi_fetch.py fetch-protein XP_022033624 -o \u002Ftmp\u002Fresult.json\nuv run scripts\u002Fncbi_fetch.py fetch-protein NP_001234567 ABC12345.1\n```\n\n### 2. Fetch Nucleotide by Accession\n\nFetches nucleotide FASTA from NCBI by accession.\n\n```bash\nuv run scripts\u002Fncbi_fetch.py fetch-nucleotide MK034466 -o \u002Ftmp\u002Fresult.json\n```\n\n### 3. CDS Translate\n\nFetches a CDS\u002Fnucleotide accession and translates to protein sequence. Tries\nthree approaches in order: 1. NCBI's pre-translated CDS protein (`fasta_cds_aa`)\n\n2. GenBank XML CDS annotation translations 3. Raw nucleotide → 6-frame ORF\nfinding\n\n```bash\nuv run scripts\u002Fncbi_fetch.py cds-translate MK034466 -o \u002Ftmp\u002Fresult.json\nuv run scripts\u002Fncbi_fetch.py cds-translate HQ662330 --target-length 1043\n```\n\nIf the accession is a **genomic record** (not mRNA\u002FCDS), the tool will report\n`is_genomic: true` so you can fall back to a homology-based approach instead.\n\n### 4. Search Any Database\n\nFree-text search using Entrez query syntax. Supports all NCBI databases.\n\n```bash\n# Search protein database\nuv run scripts\u002Fncbi_fetch.py search \"WRR4B[Gene Name] AND Arabidopsis[Organism]\" \\\n  --database protein --retmax 5 --fetch-sequences\n\n# Search nucleotide database\nuv run scripts\u002Fncbi_fetch.py search \"Rz2[Gene Name] AND Beta vulgaris[Organism]\" \\\n  --database nuccore --retmax 10\n\n# Search with patent filter\nuv run scripts\u002Fncbi_fetch.py search \"disease resistance AND Solanum[Organism] AND patent[Properties]\" \\\n  --database protein --fetch-sequences\n\n# Search by sequence length\nuv run scripts\u002Fncbi_fetch.py search '\"Oryza sativa\"[Organism] AND 1043[SLEN]' \\\n  --database protein --fetch-sequences --retmax 50\n```\n\n### 5. Cross-Database Links (elink)\n\nFollow NCBI's cross-database links (e.g., PubMed article → linked proteins).\n\n```bash\nuv run scripts\u002Fncbi_fetch.py elink 24896089 --dbfrom pubmed --db protein \\\n  --fetch-sequences -o \u002Ftmp\u002Flinked.json\n```\n\n### 6. Gene + Organism Search\n\nSearches for protein sequences by gene name and organism. Searches NCBI Protein\nwith `[Gene Name]` and `[Organism]` qualifiers.\n\n```bash\nuv run scripts\u002Fncbi_fetch.py gene-protein WRR4B --organism \"Arabidopsis thaliana\"\nuv run scripts\u002Fncbi_fetch.py gene-protein Pikh-2 --organism \"Oryza sativa\" \\\n  --target-length 1043 -o \u002Ftmp\u002Fresult.json\n```\n\n### 7. Locus Tag Search\n\nSearches by locus tag in both NCBI Protein and Nuccore databases. Extracts CDS\ntranslations from GenBank XML when direct protein hits aren't available.\n\n```bash\nuv run scripts\u002Fncbi_fetch.py locus-protein At1g56540 --organism \"Arabidopsis thaliana\"\nuv run scripts\u002Fncbi_fetch.py locus-protein Niben101Scf02422g02015.1 \\\n  --organism \"Nicotiana benthamiana\" -o \u002Ftmp\u002Fresult.json\n```\n\n### 8. PubMed-Linked Proteins\n\nFinds protein sequences linked to a PubMed article. Searches NCBI Protein by\nPMID, follows elink PubMed→Protein, and extracts CDS translations from linked\nNuccore records.\n\n```bash\nuv run scripts\u002Fncbi_fetch.py pubmed-proteins 30692254 --identifier WRR4B\nuv run scripts\u002Fncbi_fetch.py pubmed-proteins 24896089 --identifier \"K2\" \\\n  -o \u002Ftmp\u002Fresult.json\n```\n\n### 9. Patent Sequence Search\n\nTwo modes:\n\n**By patent number** — fetches all protein sequences from a specific patent:\n`bash uv run scripts\u002Fncbi_fetch.py patent-search --patent-number US10123456 -o\n\u002Ftmp\u002Fpatent.json`\n\n**By keywords** — searches NCBI Protein with `patent[Properties]` filter: `bash\nuv run scripts\u002Fncbi_fetch.py patent-search --keywords WRR4B Albugo --organism\n\"Arabidopsis thaliana\" -o \u002Ftmp\u002Fpatent.json`\n\n> [!IMPORTANT] **Patent convention**: In molecular biology patents, SEQ ID NO: 1\n> is typically the DNA sequence and SEQ ID NO: 2 is the primary protein. Higher\n> SEQ ID NOs are variants or related sequences. Prefer Sequence 2 when selecting\n> the primary protein of interest.\n\n### 10. Organism + Length Search\n\nLast-resort search when only organism and expected protein length are known.\nUses NCBI's `[SLEN]` filter for exact length matching.\n\n```bash\nuv run scripts\u002Fncbi_fetch.py organism-length \\\n  --organism \"Arabidopsis thaliana\" --length 1048 --retmax 50 \\\n  -o \u002Ftmp\u002Fresult.json\n```\n\n> [!NOTE] This often returns multiple candidates. Use the JSON output headers to\n> identify the correct protein.\n\n## Workflow\n\n### Standard Sequence Retrieval Cascade\n\nWhen trying to find a protein sequence, follow this priority order:\n\n1.  **Direct accession** — `fetch-protein` with GenPept\u002FRefSeq accession\n2.  **CDS translation** — `cds-translate` with nucleotide\u002FCDS accession\n3.  **PubMed-linked** — `pubmed-proteins` with PMID + gene name\n4.  **Locus lookup** — `locus-protein` with locus tag + organism\n5.  **Gene + organism** — `gene-protein` with gene name + organism\n6.  **Patent search** — `patent-search` with patent number or keywords\n7.  **Organism + length** — `organism-length` as last resort\n\n### Interpreting Results\n\n-   All subcommands return JSON with a `results` array\n-   Each result has `sequence` (AA string), `length`, and `header`\u002Fmetadata\n-   When multiple results are returned, select by:\n    -   Closest match to expected length (`target_length`)\n    -   Header relevance (matching gene name, \"disease resistance\" keywords)\n    -   Source priority (RefSeq > GenPept > patent)\n\n## Reference\n\n-   **NCBI E-utilities docs**: https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Fbooks\u002FNBK25499\u002F\n-   **Entrez search syntax**: https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Fbooks\u002FNBK49540\u002F\n-   **Database list**: protein, nuccore, gene, pubmed, pmc, biosample, etc.\n-   **Common accession formats**:\n    -   `XP_` \u002F `NP_` — NCBI RefSeq protein\n    -   `AAA` to `AZZ` + digits — GenPept (translated GenBank)\n    -   `MK`, `MN`, `HQ`, etc. + digits — GenBank nucleotide\n    -   `ENSG`, `ENST`, `ENSP` — Ensembl (use `ensembl-database` skill instead)\n    -   `Q`, `P`, `O` + digits — UniProt (use `uniprot-database` skill instead)\n",{"data":37,"body":38},{"name":4,"description":6},{"type":39,"children":40},"root",[41,49,56,179,185,226,232,238,351,357,371,384,391,396,479,485,490,530,536,549,557,631,651,657,662,979,985,990,1062,1068,1089,1206,1212,1217,1322,1328,1333,1431,1437,1442,1458,1482,1503,1509,1522,1606,1619,1625,1631,1636,1752,1758,1833,1839,2025],{"type":42,"tag":43,"props":44,"children":45},"element","h1",{"id":4},[46],{"type":47,"value":48},"text","NCBI Sequence Fetch",{"type":42,"tag":50,"props":51,"children":53},"h2",{"id":52},"prerequisites",[54],{"type":47,"value":55},"Prerequisites",{"type":42,"tag":57,"props":58,"children":59},"ol",{},[60,91,119,142],{"type":42,"tag":61,"props":62,"children":63},"li",{},[64,75,77,82,84,89],{"type":42,"tag":65,"props":66,"children":67},"strong",{},[68],{"type":42,"tag":69,"props":70,"children":72},"code",{"className":71},[],[73],{"type":47,"value":74},"uv",{"type":47,"value":76},": Read the ",{"type":42,"tag":69,"props":78,"children":80},{"className":79},[],[81],{"type":47,"value":74},{"type":47,"value":83}," skill and follow its Setup instructions to ensure\n",{"type":42,"tag":69,"props":85,"children":87},{"className":86},[],[88],{"type":47,"value":74},{"type":47,"value":90}," is installed and on PATH.",{"type":42,"tag":61,"props":92,"children":93},{},[94,99,101,109,111,117],{"type":42,"tag":65,"props":95,"children":96},{},[97],{"type":47,"value":98},"User Notification",{"type":47,"value":100},": If .licenses\u002Fncbi_sequence_fetch_LICENSE.txt does not\nalready exist in the workspace root directory then (1) prominently notify\nthe user to check the terms at ",{"type":42,"tag":102,"props":103,"children":107},"a",{"href":104,"rel":105},"https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002F",[106],"nofollow",[108],{"type":47,"value":104},{"type":47,"value":110}," and\n",{"type":42,"tag":102,"props":112,"children":115},{"href":113,"rel":114},"https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Fhome\u002Fabout\u002Fpolicies\u002F",[106],[116],{"type":47,"value":113},{"type":47,"value":118},", then (2) create the file\nrecording the notification text and timestamp.",{"type":42,"tag":61,"props":120,"children":121},{},[122,133,135,140],{"type":42,"tag":65,"props":123,"children":124},{},[125,131],{"type":42,"tag":69,"props":126,"children":128},{"className":127},[],[129],{"type":47,"value":130},".env",{"type":47,"value":132}," file",{"type":47,"value":134},": Make sure the ",{"type":42,"tag":69,"props":136,"children":138},{"className":137},[],[139],{"type":47,"value":130},{"type":47,"value":141}," file exists in your home directory.\nCreate one if it does not exist.",{"type":42,"tag":61,"props":143,"children":144},{},[145,154,156,162,164,169,171,177],{"type":42,"tag":65,"props":146,"children":147},{},[148],{"type":42,"tag":69,"props":149,"children":151},{"className":150},[],[152],{"type":47,"value":153},"NCBI_API_KEY",{"type":47,"value":155}," (optional): Raises the NCBI rate limit from 3 to 10\nrequests\u002Fsecond. The skill works without it, but a key is recommended if the\nuser plans many queries or encounters a 429 error. You can register for a\nkey for free at ",{"type":42,"tag":102,"props":157,"children":160},{"href":158,"rel":159},"https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Faccount\u002Fsettings\u002F",[106],[161],{"type":47,"value":158},{"type":47,"value":163},". You ",{"type":42,"tag":65,"props":165,"children":166},{},[167],{"type":47,"value":168},"MUST",{"type":47,"value":170},"\nuse the safe credentials protocol in the ",{"type":42,"tag":69,"props":172,"children":174},{"className":173},[],[175],{"type":47,"value":176},"credentials",{"type":47,"value":178}," skill to check for\nand request this key if this skill looks relevant to the user's request.",{"type":42,"tag":50,"props":180,"children":182},{"id":181},"core-rules",[183],{"type":47,"value":184},"Core Rules",{"type":42,"tag":186,"props":187,"children":188},"ul",{},[189,199,216],{"type":42,"tag":61,"props":190,"children":191},{},[192,197],{"type":42,"tag":65,"props":193,"children":194},{},[195],{"type":47,"value":196},"Use the Wrapper",{"type":47,"value":198},": ALWAYS execute the provided helper scripts to query the\ndatabase rather than accessing the database directly. The scripts\nautomatically enforce the required rate limit gracefully.",{"type":42,"tag":61,"props":200,"children":201},{},[202,207,209,214],{"type":42,"tag":65,"props":203,"children":204},{},[205],{"type":47,"value":206},"API Key Support",{"type":47,"value":208},": If the user provides an ",{"type":42,"tag":69,"props":210,"children":212},{"className":211},[],[213],{"type":47,"value":153},{"type":47,"value":215}," in their\nenvironment, the query speed limits are automatically increased\nsignificantly.",{"type":42,"tag":61,"props":217,"children":218},{},[219,224],{"type":42,"tag":65,"props":220,"children":221},{},[222],{"type":47,"value":223},"Notification",{"type":47,"value":225},": If this skill is used, ensure this is mentioned in the\noutput.",{"type":42,"tag":50,"props":227,"children":229},{"id":228},"overview",[230],{"type":47,"value":231},"Overview",{"type":42,"tag":233,"props":234,"children":235},"p",{},[236],{"type":47,"value":237},"Wraps NCBI's Entrez E-utilities (efetch, esearch, elink, esummary) for\nretrieving protein and nucleotide sequences. Provides 10 subcommands covering\nthe full range of sequence retrieval workflows:",{"type":42,"tag":186,"props":239,"children":240},{},[241,252,263,274,285,296,307,318,329,340],{"type":42,"tag":61,"props":242,"children":243},{},[244,250],{"type":42,"tag":69,"props":245,"children":247},{"className":246},[],[248],{"type":47,"value":249},"fetch-protein",{"type":47,"value":251}," — Direct protein accession lookup (GenPept, RefSeq)",{"type":42,"tag":61,"props":253,"children":254},{},[255,261],{"type":42,"tag":69,"props":256,"children":258},{"className":257},[],[259],{"type":47,"value":260},"fetch-nucleotide",{"type":47,"value":262}," — Direct nucleotide accession lookup",{"type":42,"tag":61,"props":264,"children":265},{},[266,272],{"type":42,"tag":69,"props":267,"children":269},{"className":268},[],[270],{"type":47,"value":271},"cds-translate",{"type":47,"value":273}," — Fetch CDS and translate to protein (3 methods)",{"type":42,"tag":61,"props":275,"children":276},{},[277,283],{"type":42,"tag":69,"props":278,"children":280},{"className":279},[],[281],{"type":47,"value":282},"search",{"type":47,"value":284}," — Free-text search of any NCBI database",{"type":42,"tag":61,"props":286,"children":287},{},[288,294],{"type":42,"tag":69,"props":289,"children":291},{"className":290},[],[292],{"type":47,"value":293},"elink",{"type":47,"value":295}," — Follow cross-database links (PubMed→Protein, etc.)",{"type":42,"tag":61,"props":297,"children":298},{},[299,305],{"type":42,"tag":69,"props":300,"children":302},{"className":301},[],[303],{"type":47,"value":304},"gene-protein",{"type":47,"value":306}," — Search protein by gene name + organism",{"type":42,"tag":61,"props":308,"children":309},{},[310,316],{"type":42,"tag":69,"props":311,"children":313},{"className":312},[],[314],{"type":47,"value":315},"locus-protein",{"type":47,"value":317}," — Search protein by locus tag + organism",{"type":42,"tag":61,"props":319,"children":320},{},[321,327],{"type":42,"tag":69,"props":322,"children":324},{"className":323},[],[325],{"type":47,"value":326},"pubmed-proteins",{"type":47,"value":328}," — Find proteins linked to a PubMed article",{"type":42,"tag":61,"props":330,"children":331},{},[332,338],{"type":42,"tag":69,"props":333,"children":335},{"className":334},[],[336],{"type":47,"value":337},"patent-search",{"type":47,"value":339}," — Extract protein sequences from patents",{"type":42,"tag":61,"props":341,"children":342},{},[343,349],{"type":42,"tag":69,"props":344,"children":346},{"className":345},[],[347],{"type":47,"value":348},"organism-length",{"type":47,"value":350}," — Last-resort search by organism + exact AA length",{"type":42,"tag":50,"props":352,"children":354},{"id":353},"utility-scripts",[355],{"type":47,"value":356},"Utility Scripts",{"type":42,"tag":233,"props":358,"children":359},{},[360,369],{"type":42,"tag":65,"props":361,"children":362},{},[363],{"type":42,"tag":69,"props":364,"children":366},{"className":365},[],[367],{"type":47,"value":368},"scripts\u002Fncbi_fetch.py",{"type":47,"value":370}," — Single script with subcommands.",{"type":42,"tag":233,"props":372,"children":373},{},[374,376,382],{"type":47,"value":375},"All subcommands write structured JSON output. Use ",{"type":42,"tag":69,"props":377,"children":379},{"className":378},[],[380],{"type":47,"value":381},"--output FILE",{"type":47,"value":383}," to save to a\nfile, or omit it to print to stdout. A human-readable summary is always printed\nto stdout.",{"type":42,"tag":385,"props":386,"children":388},"h3",{"id":387},"_1-fetch-protein-by-accession",[389],{"type":47,"value":390},"1. Fetch Protein by Accession",{"type":42,"tag":233,"props":392,"children":393},{},[394],{"type":47,"value":395},"Fetches protein FASTA from NCBI by accession (XP_, NP_, GenPept, etc.)",{"type":42,"tag":397,"props":398,"children":403},"pre",{"className":399,"code":400,"language":401,"meta":402,"style":402},"language-bash shiki shiki-themes material-theme-lighter material-theme material-theme-palenight","uv run scripts\u002Fncbi_fetch.py fetch-protein XP_022033624 -o \u002Ftmp\u002Fresult.json\nuv run scripts\u002Fncbi_fetch.py fetch-protein NP_001234567 ABC12345.1\n","bash","",[404],{"type":42,"tag":69,"props":405,"children":406},{"__ignoreMap":402},[407,449],{"type":42,"tag":408,"props":409,"children":412},"span",{"class":410,"line":411},"line",1,[413,418,424,429,434,439,444],{"type":42,"tag":408,"props":414,"children":416},{"style":415},"--shiki-light:#E2931D;--shiki-default:#FFCB6B;--shiki-dark:#FFCB6B",[417],{"type":47,"value":74},{"type":42,"tag":408,"props":419,"children":421},{"style":420},"--shiki-light:#91B859;--shiki-default:#C3E88D;--shiki-dark:#C3E88D",[422],{"type":47,"value":423}," run",{"type":42,"tag":408,"props":425,"children":426},{"style":420},[427],{"type":47,"value":428}," scripts\u002Fncbi_fetch.py",{"type":42,"tag":408,"props":430,"children":431},{"style":420},[432],{"type":47,"value":433}," fetch-protein",{"type":42,"tag":408,"props":435,"children":436},{"style":420},[437],{"type":47,"value":438}," XP_022033624",{"type":42,"tag":408,"props":440,"children":441},{"style":420},[442],{"type":47,"value":443}," -o",{"type":42,"tag":408,"props":445,"children":446},{"style":420},[447],{"type":47,"value":448}," \u002Ftmp\u002Fresult.json\n",{"type":42,"tag":408,"props":450,"children":452},{"class":410,"line":451},2,[453,457,461,465,469,474],{"type":42,"tag":408,"props":454,"children":455},{"style":415},[456],{"type":47,"value":74},{"type":42,"tag":408,"props":458,"children":459},{"style":420},[460],{"type":47,"value":423},{"type":42,"tag":408,"props":462,"children":463},{"style":420},[464],{"type":47,"value":428},{"type":42,"tag":408,"props":466,"children":467},{"style":420},[468],{"type":47,"value":433},{"type":42,"tag":408,"props":470,"children":471},{"style":420},[472],{"type":47,"value":473}," NP_001234567",{"type":42,"tag":408,"props":475,"children":476},{"style":420},[477],{"type":47,"value":478}," ABC12345.1\n",{"type":42,"tag":385,"props":480,"children":482},{"id":481},"_2-fetch-nucleotide-by-accession",[483],{"type":47,"value":484},"2. Fetch Nucleotide by Accession",{"type":42,"tag":233,"props":486,"children":487},{},[488],{"type":47,"value":489},"Fetches nucleotide FASTA from NCBI by accession.",{"type":42,"tag":397,"props":491,"children":493},{"className":399,"code":492,"language":401,"meta":402,"style":402},"uv run scripts\u002Fncbi_fetch.py fetch-nucleotide MK034466 -o \u002Ftmp\u002Fresult.json\n",[494],{"type":42,"tag":69,"props":495,"children":496},{"__ignoreMap":402},[497],{"type":42,"tag":408,"props":498,"children":499},{"class":410,"line":411},[500,504,508,512,517,522,526],{"type":42,"tag":408,"props":501,"children":502},{"style":415},[503],{"type":47,"value":74},{"type":42,"tag":408,"props":505,"children":506},{"style":420},[507],{"type":47,"value":423},{"type":42,"tag":408,"props":509,"children":510},{"style":420},[511],{"type":47,"value":428},{"type":42,"tag":408,"props":513,"children":514},{"style":420},[515],{"type":47,"value":516}," fetch-nucleotide",{"type":42,"tag":408,"props":518,"children":519},{"style":420},[520],{"type":47,"value":521}," MK034466",{"type":42,"tag":408,"props":523,"children":524},{"style":420},[525],{"type":47,"value":443},{"type":42,"tag":408,"props":527,"children":528},{"style":420},[529],{"type":47,"value":448},{"type":42,"tag":385,"props":531,"children":533},{"id":532},"_3-cds-translate",[534],{"type":47,"value":535},"3. CDS Translate",{"type":42,"tag":233,"props":537,"children":538},{},[539,541,547],{"type":47,"value":540},"Fetches a CDS\u002Fnucleotide accession and translates to protein sequence. Tries\nthree approaches in order: 1. NCBI's pre-translated CDS protein (",{"type":42,"tag":69,"props":542,"children":544},{"className":543},[],[545],{"type":47,"value":546},"fasta_cds_aa",{"type":47,"value":548},")",{"type":42,"tag":57,"props":550,"children":551},{"start":451},[552],{"type":42,"tag":61,"props":553,"children":554},{},[555],{"type":47,"value":556},"GenBank XML CDS annotation translations 3. Raw nucleotide → 6-frame ORF\nfinding",{"type":42,"tag":397,"props":558,"children":560},{"className":399,"code":559,"language":401,"meta":402,"style":402},"uv run scripts\u002Fncbi_fetch.py cds-translate MK034466 -o \u002Ftmp\u002Fresult.json\nuv run scripts\u002Fncbi_fetch.py cds-translate HQ662330 --target-length 1043\n",[561],{"type":42,"tag":69,"props":562,"children":563},{"__ignoreMap":402},[564,596],{"type":42,"tag":408,"props":565,"children":566},{"class":410,"line":411},[567,571,575,579,584,588,592],{"type":42,"tag":408,"props":568,"children":569},{"style":415},[570],{"type":47,"value":74},{"type":42,"tag":408,"props":572,"children":573},{"style":420},[574],{"type":47,"value":423},{"type":42,"tag":408,"props":576,"children":577},{"style":420},[578],{"type":47,"value":428},{"type":42,"tag":408,"props":580,"children":581},{"style":420},[582],{"type":47,"value":583}," cds-translate",{"type":42,"tag":408,"props":585,"children":586},{"style":420},[587],{"type":47,"value":521},{"type":42,"tag":408,"props":589,"children":590},{"style":420},[591],{"type":47,"value":443},{"type":42,"tag":408,"props":593,"children":594},{"style":420},[595],{"type":47,"value":448},{"type":42,"tag":408,"props":597,"children":598},{"class":410,"line":451},[599,603,607,611,615,620,625],{"type":42,"tag":408,"props":600,"children":601},{"style":415},[602],{"type":47,"value":74},{"type":42,"tag":408,"props":604,"children":605},{"style":420},[606],{"type":47,"value":423},{"type":42,"tag":408,"props":608,"children":609},{"style":420},[610],{"type":47,"value":428},{"type":42,"tag":408,"props":612,"children":613},{"style":420},[614],{"type":47,"value":583},{"type":42,"tag":408,"props":616,"children":617},{"style":420},[618],{"type":47,"value":619}," HQ662330",{"type":42,"tag":408,"props":621,"children":622},{"style":420},[623],{"type":47,"value":624}," --target-length",{"type":42,"tag":408,"props":626,"children":628},{"style":627},"--shiki-light:#F76D47;--shiki-default:#F78C6C;--shiki-dark:#F78C6C",[629],{"type":47,"value":630}," 1043\n",{"type":42,"tag":233,"props":632,"children":633},{},[634,636,641,643,649],{"type":47,"value":635},"If the accession is a ",{"type":42,"tag":65,"props":637,"children":638},{},[639],{"type":47,"value":640},"genomic record",{"type":47,"value":642}," (not mRNA\u002FCDS), the tool will report\n",{"type":42,"tag":69,"props":644,"children":646},{"className":645},[],[647],{"type":47,"value":648},"is_genomic: true",{"type":47,"value":650}," so you can fall back to a homology-based approach instead.",{"type":42,"tag":385,"props":652,"children":654},{"id":653},"_4-search-any-database",[655],{"type":47,"value":656},"4. Search Any Database",{"type":42,"tag":233,"props":658,"children":659},{},[660],{"type":47,"value":661},"Free-text search using Entrez query syntax. Supports all NCBI databases.",{"type":42,"tag":397,"props":663,"children":665},{"className":399,"code":664,"language":401,"meta":402,"style":402},"# Search protein database\nuv run scripts\u002Fncbi_fetch.py search \"WRR4B[Gene Name] AND Arabidopsis[Organism]\" \\\n  --database protein --retmax 5 --fetch-sequences\n\n# Search nucleotide database\nuv run scripts\u002Fncbi_fetch.py search \"Rz2[Gene Name] AND Beta vulgaris[Organism]\" \\\n  --database nuccore --retmax 10\n\n# Search with patent filter\nuv run scripts\u002Fncbi_fetch.py search \"disease resistance AND Solanum[Organism] AND patent[Properties]\" \\\n  --database protein --fetch-sequences\n\n# Search by sequence length\nuv run scripts\u002Fncbi_fetch.py search '\"Oryza sativa\"[Organism] AND 1043[SLEN]' \\\n  --database protein --fetch-sequences --retmax 50\n",[666],{"type":42,"tag":69,"props":667,"children":668},{"__ignoreMap":402},[669,678,720,749,759,768,805,827,835,844,881,897,905,914,953],{"type":42,"tag":408,"props":670,"children":671},{"class":410,"line":411},[672],{"type":42,"tag":408,"props":673,"children":675},{"style":674},"--shiki-light:#90A4AE;--shiki-light-font-style:italic;--shiki-default:#546E7A;--shiki-default-font-style:italic;--shiki-dark:#676E95;--shiki-dark-font-style:italic",[676],{"type":47,"value":677},"# Search protein database\n",{"type":42,"tag":408,"props":679,"children":680},{"class":410,"line":451},[681,685,689,693,698,704,709,714],{"type":42,"tag":408,"props":682,"children":683},{"style":415},[684],{"type":47,"value":74},{"type":42,"tag":408,"props":686,"children":687},{"style":420},[688],{"type":47,"value":423},{"type":42,"tag":408,"props":690,"children":691},{"style":420},[692],{"type":47,"value":428},{"type":42,"tag":408,"props":694,"children":695},{"style":420},[696],{"type":47,"value":697}," search",{"type":42,"tag":408,"props":699,"children":701},{"style":700},"--shiki-light:#39ADB5;--shiki-default:#89DDFF;--shiki-dark:#89DDFF",[702],{"type":47,"value":703}," \"",{"type":42,"tag":408,"props":705,"children":706},{"style":420},[707],{"type":47,"value":708},"WRR4B[Gene Name] AND Arabidopsis[Organism]",{"type":42,"tag":408,"props":710,"children":711},{"style":700},[712],{"type":47,"value":713},"\"",{"type":42,"tag":408,"props":715,"children":717},{"style":716},"--shiki-light:#90A4AE;--shiki-default:#EEFFFF;--shiki-dark:#BABED8",[718],{"type":47,"value":719}," \\\n",{"type":42,"tag":408,"props":721,"children":723},{"class":410,"line":722},3,[724,729,734,739,744],{"type":42,"tag":408,"props":725,"children":726},{"style":420},[727],{"type":47,"value":728},"  --database",{"type":42,"tag":408,"props":730,"children":731},{"style":420},[732],{"type":47,"value":733}," protein",{"type":42,"tag":408,"props":735,"children":736},{"style":420},[737],{"type":47,"value":738}," --retmax",{"type":42,"tag":408,"props":740,"children":741},{"style":627},[742],{"type":47,"value":743}," 5",{"type":42,"tag":408,"props":745,"children":746},{"style":420},[747],{"type":47,"value":748}," --fetch-sequences\n",{"type":42,"tag":408,"props":750,"children":752},{"class":410,"line":751},4,[753],{"type":42,"tag":408,"props":754,"children":756},{"emptyLinePlaceholder":755},true,[757],{"type":47,"value":758},"\n",{"type":42,"tag":408,"props":760,"children":762},{"class":410,"line":761},5,[763],{"type":42,"tag":408,"props":764,"children":765},{"style":674},[766],{"type":47,"value":767},"# Search nucleotide database\n",{"type":42,"tag":408,"props":769,"children":771},{"class":410,"line":770},6,[772,776,780,784,788,792,797,801],{"type":42,"tag":408,"props":773,"children":774},{"style":415},[775],{"type":47,"value":74},{"type":42,"tag":408,"props":777,"children":778},{"style":420},[779],{"type":47,"value":423},{"type":42,"tag":408,"props":781,"children":782},{"style":420},[783],{"type":47,"value":428},{"type":42,"tag":408,"props":785,"children":786},{"style":420},[787],{"type":47,"value":697},{"type":42,"tag":408,"props":789,"children":790},{"style":700},[791],{"type":47,"value":703},{"type":42,"tag":408,"props":793,"children":794},{"style":420},[795],{"type":47,"value":796},"Rz2[Gene Name] AND Beta vulgaris[Organism]",{"type":42,"tag":408,"props":798,"children":799},{"style":700},[800],{"type":47,"value":713},{"type":42,"tag":408,"props":802,"children":803},{"style":716},[804],{"type":47,"value":719},{"type":42,"tag":408,"props":806,"children":808},{"class":410,"line":807},7,[809,813,818,822],{"type":42,"tag":408,"props":810,"children":811},{"style":420},[812],{"type":47,"value":728},{"type":42,"tag":408,"props":814,"children":815},{"style":420},[816],{"type":47,"value":817}," nuccore",{"type":42,"tag":408,"props":819,"children":820},{"style":420},[821],{"type":47,"value":738},{"type":42,"tag":408,"props":823,"children":824},{"style":627},[825],{"type":47,"value":826}," 10\n",{"type":42,"tag":408,"props":828,"children":830},{"class":410,"line":829},8,[831],{"type":42,"tag":408,"props":832,"children":833},{"emptyLinePlaceholder":755},[834],{"type":47,"value":758},{"type":42,"tag":408,"props":836,"children":838},{"class":410,"line":837},9,[839],{"type":42,"tag":408,"props":840,"children":841},{"style":674},[842],{"type":47,"value":843},"# Search with patent filter\n",{"type":42,"tag":408,"props":845,"children":847},{"class":410,"line":846},10,[848,852,856,860,864,868,873,877],{"type":42,"tag":408,"props":849,"children":850},{"style":415},[851],{"type":47,"value":74},{"type":42,"tag":408,"props":853,"children":854},{"style":420},[855],{"type":47,"value":423},{"type":42,"tag":408,"props":857,"children":858},{"style":420},[859],{"type":47,"value":428},{"type":42,"tag":408,"props":861,"children":862},{"style":420},[863],{"type":47,"value":697},{"type":42,"tag":408,"props":865,"children":866},{"style":700},[867],{"type":47,"value":703},{"type":42,"tag":408,"props":869,"children":870},{"style":420},[871],{"type":47,"value":872},"disease resistance AND Solanum[Organism] AND patent[Properties]",{"type":42,"tag":408,"props":874,"children":875},{"style":700},[876],{"type":47,"value":713},{"type":42,"tag":408,"props":878,"children":879},{"style":716},[880],{"type":47,"value":719},{"type":42,"tag":408,"props":882,"children":884},{"class":410,"line":883},11,[885,889,893],{"type":42,"tag":408,"props":886,"children":887},{"style":420},[888],{"type":47,"value":728},{"type":42,"tag":408,"props":890,"children":891},{"style":420},[892],{"type":47,"value":733},{"type":42,"tag":408,"props":894,"children":895},{"style":420},[896],{"type":47,"value":748},{"type":42,"tag":408,"props":898,"children":900},{"class":410,"line":899},12,[901],{"type":42,"tag":408,"props":902,"children":903},{"emptyLinePlaceholder":755},[904],{"type":47,"value":758},{"type":42,"tag":408,"props":906,"children":908},{"class":410,"line":907},13,[909],{"type":42,"tag":408,"props":910,"children":911},{"style":674},[912],{"type":47,"value":913},"# Search by sequence length\n",{"type":42,"tag":408,"props":915,"children":917},{"class":410,"line":916},14,[918,922,926,930,934,939,944,949],{"type":42,"tag":408,"props":919,"children":920},{"style":415},[921],{"type":47,"value":74},{"type":42,"tag":408,"props":923,"children":924},{"style":420},[925],{"type":47,"value":423},{"type":42,"tag":408,"props":927,"children":928},{"style":420},[929],{"type":47,"value":428},{"type":42,"tag":408,"props":931,"children":932},{"style":420},[933],{"type":47,"value":697},{"type":42,"tag":408,"props":935,"children":936},{"style":700},[937],{"type":47,"value":938}," '",{"type":42,"tag":408,"props":940,"children":941},{"style":420},[942],{"type":47,"value":943},"\"Oryza sativa\"[Organism] AND 1043[SLEN]",{"type":42,"tag":408,"props":945,"children":946},{"style":700},[947],{"type":47,"value":948},"'",{"type":42,"tag":408,"props":950,"children":951},{"style":716},[952],{"type":47,"value":719},{"type":42,"tag":408,"props":954,"children":956},{"class":410,"line":955},15,[957,961,965,970,974],{"type":42,"tag":408,"props":958,"children":959},{"style":420},[960],{"type":47,"value":728},{"type":42,"tag":408,"props":962,"children":963},{"style":420},[964],{"type":47,"value":733},{"type":42,"tag":408,"props":966,"children":967},{"style":420},[968],{"type":47,"value":969}," --fetch-sequences",{"type":42,"tag":408,"props":971,"children":972},{"style":420},[973],{"type":47,"value":738},{"type":42,"tag":408,"props":975,"children":976},{"style":627},[977],{"type":47,"value":978}," 50\n",{"type":42,"tag":385,"props":980,"children":982},{"id":981},"_5-cross-database-links-elink",[983],{"type":47,"value":984},"5. Cross-Database Links (elink)",{"type":42,"tag":233,"props":986,"children":987},{},[988],{"type":47,"value":989},"Follow NCBI's cross-database links (e.g., PubMed article → linked proteins).",{"type":42,"tag":397,"props":991,"children":993},{"className":399,"code":992,"language":401,"meta":402,"style":402},"uv run scripts\u002Fncbi_fetch.py elink 24896089 --dbfrom pubmed --db protein \\\n  --fetch-sequences -o \u002Ftmp\u002Flinked.json\n",[994],{"type":42,"tag":69,"props":995,"children":996},{"__ignoreMap":402},[997,1045],{"type":42,"tag":408,"props":998,"children":999},{"class":410,"line":411},[1000,1004,1008,1012,1017,1022,1027,1032,1037,1041],{"type":42,"tag":408,"props":1001,"children":1002},{"style":415},[1003],{"type":47,"value":74},{"type":42,"tag":408,"props":1005,"children":1006},{"style":420},[1007],{"type":47,"value":423},{"type":42,"tag":408,"props":1009,"children":1010},{"style":420},[1011],{"type":47,"value":428},{"type":42,"tag":408,"props":1013,"children":1014},{"style":420},[1015],{"type":47,"value":1016}," elink",{"type":42,"tag":408,"props":1018,"children":1019},{"style":627},[1020],{"type":47,"value":1021}," 24896089",{"type":42,"tag":408,"props":1023,"children":1024},{"style":420},[1025],{"type":47,"value":1026}," --dbfrom",{"type":42,"tag":408,"props":1028,"children":1029},{"style":420},[1030],{"type":47,"value":1031}," pubmed",{"type":42,"tag":408,"props":1033,"children":1034},{"style":420},[1035],{"type":47,"value":1036}," --db",{"type":42,"tag":408,"props":1038,"children":1039},{"style":420},[1040],{"type":47,"value":733},{"type":42,"tag":408,"props":1042,"children":1043},{"style":716},[1044],{"type":47,"value":719},{"type":42,"tag":408,"props":1046,"children":1047},{"class":410,"line":451},[1048,1053,1057],{"type":42,"tag":408,"props":1049,"children":1050},{"style":420},[1051],{"type":47,"value":1052},"  --fetch-sequences",{"type":42,"tag":408,"props":1054,"children":1055},{"style":420},[1056],{"type":47,"value":443},{"type":42,"tag":408,"props":1058,"children":1059},{"style":420},[1060],{"type":47,"value":1061}," \u002Ftmp\u002Flinked.json\n",{"type":42,"tag":385,"props":1063,"children":1065},{"id":1064},"_6-gene-organism-search",[1066],{"type":47,"value":1067},"6. Gene + Organism Search",{"type":42,"tag":233,"props":1069,"children":1070},{},[1071,1073,1079,1081,1087],{"type":47,"value":1072},"Searches for protein sequences by gene name and organism. Searches NCBI Protein\nwith ",{"type":42,"tag":69,"props":1074,"children":1076},{"className":1075},[],[1077],{"type":47,"value":1078},"[Gene Name]",{"type":47,"value":1080}," and ",{"type":42,"tag":69,"props":1082,"children":1084},{"className":1083},[],[1085],{"type":47,"value":1086},"[Organism]",{"type":47,"value":1088}," qualifiers.",{"type":42,"tag":397,"props":1090,"children":1092},{"className":399,"code":1091,"language":401,"meta":402,"style":402},"uv run scripts\u002Fncbi_fetch.py gene-protein WRR4B --organism \"Arabidopsis thaliana\"\nuv run scripts\u002Fncbi_fetch.py gene-protein Pikh-2 --organism \"Oryza sativa\" \\\n  --target-length 1043 -o \u002Ftmp\u002Fresult.json\n",[1093],{"type":42,"tag":69,"props":1094,"children":1095},{"__ignoreMap":402},[1096,1140,1185],{"type":42,"tag":408,"props":1097,"children":1098},{"class":410,"line":411},[1099,1103,1107,1111,1116,1121,1126,1130,1135],{"type":42,"tag":408,"props":1100,"children":1101},{"style":415},[1102],{"type":47,"value":74},{"type":42,"tag":408,"props":1104,"children":1105},{"style":420},[1106],{"type":47,"value":423},{"type":42,"tag":408,"props":1108,"children":1109},{"style":420},[1110],{"type":47,"value":428},{"type":42,"tag":408,"props":1112,"children":1113},{"style":420},[1114],{"type":47,"value":1115}," gene-protein",{"type":42,"tag":408,"props":1117,"children":1118},{"style":420},[1119],{"type":47,"value":1120}," WRR4B",{"type":42,"tag":408,"props":1122,"children":1123},{"style":420},[1124],{"type":47,"value":1125}," --organism",{"type":42,"tag":408,"props":1127,"children":1128},{"style":700},[1129],{"type":47,"value":703},{"type":42,"tag":408,"props":1131,"children":1132},{"style":420},[1133],{"type":47,"value":1134},"Arabidopsis thaliana",{"type":42,"tag":408,"props":1136,"children":1137},{"style":700},[1138],{"type":47,"value":1139},"\"\n",{"type":42,"tag":408,"props":1141,"children":1142},{"class":410,"line":451},[1143,1147,1151,1155,1159,1164,1168,1172,1177,1181],{"type":42,"tag":408,"props":1144,"children":1145},{"style":415},[1146],{"type":47,"value":74},{"type":42,"tag":408,"props":1148,"children":1149},{"style":420},[1150],{"type":47,"value":423},{"type":42,"tag":408,"props":1152,"children":1153},{"style":420},[1154],{"type":47,"value":428},{"type":42,"tag":408,"props":1156,"children":1157},{"style":420},[1158],{"type":47,"value":1115},{"type":42,"tag":408,"props":1160,"children":1161},{"style":420},[1162],{"type":47,"value":1163}," Pikh-2",{"type":42,"tag":408,"props":1165,"children":1166},{"style":420},[1167],{"type":47,"value":1125},{"type":42,"tag":408,"props":1169,"children":1170},{"style":700},[1171],{"type":47,"value":703},{"type":42,"tag":408,"props":1173,"children":1174},{"style":420},[1175],{"type":47,"value":1176},"Oryza sativa",{"type":42,"tag":408,"props":1178,"children":1179},{"style":700},[1180],{"type":47,"value":713},{"type":42,"tag":408,"props":1182,"children":1183},{"style":716},[1184],{"type":47,"value":719},{"type":42,"tag":408,"props":1186,"children":1187},{"class":410,"line":722},[1188,1193,1198,1202],{"type":42,"tag":408,"props":1189,"children":1190},{"style":420},[1191],{"type":47,"value":1192},"  --target-length",{"type":42,"tag":408,"props":1194,"children":1195},{"style":627},[1196],{"type":47,"value":1197}," 1043",{"type":42,"tag":408,"props":1199,"children":1200},{"style":420},[1201],{"type":47,"value":443},{"type":42,"tag":408,"props":1203,"children":1204},{"style":420},[1205],{"type":47,"value":448},{"type":42,"tag":385,"props":1207,"children":1209},{"id":1208},"_7-locus-tag-search",[1210],{"type":47,"value":1211},"7. Locus Tag Search",{"type":42,"tag":233,"props":1213,"children":1214},{},[1215],{"type":47,"value":1216},"Searches by locus tag in both NCBI Protein and Nuccore databases. Extracts CDS\ntranslations from GenBank XML when direct protein hits aren't available.",{"type":42,"tag":397,"props":1218,"children":1220},{"className":399,"code":1219,"language":401,"meta":402,"style":402},"uv run scripts\u002Fncbi_fetch.py locus-protein At1g56540 --organism \"Arabidopsis thaliana\"\nuv run scripts\u002Fncbi_fetch.py locus-protein Niben101Scf02422g02015.1 \\\n  --organism \"Nicotiana benthamiana\" -o \u002Ftmp\u002Fresult.json\n",[1221],{"type":42,"tag":69,"props":1222,"children":1223},{"__ignoreMap":402},[1224,1265,1293],{"type":42,"tag":408,"props":1225,"children":1226},{"class":410,"line":411},[1227,1231,1235,1239,1244,1249,1253,1257,1261],{"type":42,"tag":408,"props":1228,"children":1229},{"style":415},[1230],{"type":47,"value":74},{"type":42,"tag":408,"props":1232,"children":1233},{"style":420},[1234],{"type":47,"value":423},{"type":42,"tag":408,"props":1236,"children":1237},{"style":420},[1238],{"type":47,"value":428},{"type":42,"tag":408,"props":1240,"children":1241},{"style":420},[1242],{"type":47,"value":1243}," locus-protein",{"type":42,"tag":408,"props":1245,"children":1246},{"style":420},[1247],{"type":47,"value":1248}," At1g56540",{"type":42,"tag":408,"props":1250,"children":1251},{"style":420},[1252],{"type":47,"value":1125},{"type":42,"tag":408,"props":1254,"children":1255},{"style":700},[1256],{"type":47,"value":703},{"type":42,"tag":408,"props":1258,"children":1259},{"style":420},[1260],{"type":47,"value":1134},{"type":42,"tag":408,"props":1262,"children":1263},{"style":700},[1264],{"type":47,"value":1139},{"type":42,"tag":408,"props":1266,"children":1267},{"class":410,"line":451},[1268,1272,1276,1280,1284,1289],{"type":42,"tag":408,"props":1269,"children":1270},{"style":415},[1271],{"type":47,"value":74},{"type":42,"tag":408,"props":1273,"children":1274},{"style":420},[1275],{"type":47,"value":423},{"type":42,"tag":408,"props":1277,"children":1278},{"style":420},[1279],{"type":47,"value":428},{"type":42,"tag":408,"props":1281,"children":1282},{"style":420},[1283],{"type":47,"value":1243},{"type":42,"tag":408,"props":1285,"children":1286},{"style":420},[1287],{"type":47,"value":1288}," Niben101Scf02422g02015.1",{"type":42,"tag":408,"props":1290,"children":1291},{"style":716},[1292],{"type":47,"value":719},{"type":42,"tag":408,"props":1294,"children":1295},{"class":410,"line":722},[1296,1301,1305,1310,1314,1318],{"type":42,"tag":408,"props":1297,"children":1298},{"style":420},[1299],{"type":47,"value":1300},"  --organism",{"type":42,"tag":408,"props":1302,"children":1303},{"style":700},[1304],{"type":47,"value":703},{"type":42,"tag":408,"props":1306,"children":1307},{"style":420},[1308],{"type":47,"value":1309},"Nicotiana benthamiana",{"type":42,"tag":408,"props":1311,"children":1312},{"style":700},[1313],{"type":47,"value":713},{"type":42,"tag":408,"props":1315,"children":1316},{"style":420},[1317],{"type":47,"value":443},{"type":42,"tag":408,"props":1319,"children":1320},{"style":420},[1321],{"type":47,"value":448},{"type":42,"tag":385,"props":1323,"children":1325},{"id":1324},"_8-pubmed-linked-proteins",[1326],{"type":47,"value":1327},"8. PubMed-Linked Proteins",{"type":42,"tag":233,"props":1329,"children":1330},{},[1331],{"type":47,"value":1332},"Finds protein sequences linked to a PubMed article. Searches NCBI Protein by\nPMID, follows elink PubMed→Protein, and extracts CDS translations from linked\nNuccore records.",{"type":42,"tag":397,"props":1334,"children":1336},{"className":399,"code":1335,"language":401,"meta":402,"style":402},"uv run scripts\u002Fncbi_fetch.py pubmed-proteins 30692254 --identifier WRR4B\nuv run scripts\u002Fncbi_fetch.py pubmed-proteins 24896089 --identifier \"K2\" \\\n  -o \u002Ftmp\u002Fresult.json\n",[1337],{"type":42,"tag":69,"props":1338,"children":1339},{"__ignoreMap":402},[1340,1375,1419],{"type":42,"tag":408,"props":1341,"children":1342},{"class":410,"line":411},[1343,1347,1351,1355,1360,1365,1370],{"type":42,"tag":408,"props":1344,"children":1345},{"style":415},[1346],{"type":47,"value":74},{"type":42,"tag":408,"props":1348,"children":1349},{"style":420},[1350],{"type":47,"value":423},{"type":42,"tag":408,"props":1352,"children":1353},{"style":420},[1354],{"type":47,"value":428},{"type":42,"tag":408,"props":1356,"children":1357},{"style":420},[1358],{"type":47,"value":1359}," pubmed-proteins",{"type":42,"tag":408,"props":1361,"children":1362},{"style":627},[1363],{"type":47,"value":1364}," 30692254",{"type":42,"tag":408,"props":1366,"children":1367},{"style":420},[1368],{"type":47,"value":1369}," --identifier",{"type":42,"tag":408,"props":1371,"children":1372},{"style":420},[1373],{"type":47,"value":1374}," WRR4B\n",{"type":42,"tag":408,"props":1376,"children":1377},{"class":410,"line":451},[1378,1382,1386,1390,1394,1398,1402,1406,1411,1415],{"type":42,"tag":408,"props":1379,"children":1380},{"style":415},[1381],{"type":47,"value":74},{"type":42,"tag":408,"props":1383,"children":1384},{"style":420},[1385],{"type":47,"value":423},{"type":42,"tag":408,"props":1387,"children":1388},{"style":420},[1389],{"type":47,"value":428},{"type":42,"tag":408,"props":1391,"children":1392},{"style":420},[1393],{"type":47,"value":1359},{"type":42,"tag":408,"props":1395,"children":1396},{"style":627},[1397],{"type":47,"value":1021},{"type":42,"tag":408,"props":1399,"children":1400},{"style":420},[1401],{"type":47,"value":1369},{"type":42,"tag":408,"props":1403,"children":1404},{"style":700},[1405],{"type":47,"value":703},{"type":42,"tag":408,"props":1407,"children":1408},{"style":420},[1409],{"type":47,"value":1410},"K2",{"type":42,"tag":408,"props":1412,"children":1413},{"style":700},[1414],{"type":47,"value":713},{"type":42,"tag":408,"props":1416,"children":1417},{"style":716},[1418],{"type":47,"value":719},{"type":42,"tag":408,"props":1420,"children":1421},{"class":410,"line":722},[1422,1427],{"type":42,"tag":408,"props":1423,"children":1424},{"style":420},[1425],{"type":47,"value":1426},"  -o",{"type":42,"tag":408,"props":1428,"children":1429},{"style":420},[1430],{"type":47,"value":448},{"type":42,"tag":385,"props":1432,"children":1434},{"id":1433},"_9-patent-sequence-search",[1435],{"type":47,"value":1436},"9. Patent Sequence Search",{"type":42,"tag":233,"props":1438,"children":1439},{},[1440],{"type":47,"value":1441},"Two modes:",{"type":42,"tag":233,"props":1443,"children":1444},{},[1445,1450,1452],{"type":42,"tag":65,"props":1446,"children":1447},{},[1448],{"type":47,"value":1449},"By patent number",{"type":47,"value":1451}," — fetches all protein sequences from a specific patent:\n",{"type":42,"tag":69,"props":1453,"children":1455},{"className":1454},[],[1456],{"type":47,"value":1457},"bash uv run scripts\u002Fncbi_fetch.py patent-search --patent-number US10123456 -o \u002Ftmp\u002Fpatent.json",{"type":42,"tag":233,"props":1459,"children":1460},{},[1461,1466,1468,1474,1476],{"type":42,"tag":65,"props":1462,"children":1463},{},[1464],{"type":47,"value":1465},"By keywords",{"type":47,"value":1467}," — searches NCBI Protein with ",{"type":42,"tag":69,"props":1469,"children":1471},{"className":1470},[],[1472],{"type":47,"value":1473},"patent[Properties]",{"type":47,"value":1475}," filter: ",{"type":42,"tag":69,"props":1477,"children":1479},{"className":1478},[],[1480],{"type":47,"value":1481},"bash uv run scripts\u002Fncbi_fetch.py patent-search --keywords WRR4B Albugo --organism \"Arabidopsis thaliana\" -o \u002Ftmp\u002Fpatent.json",{"type":42,"tag":1483,"props":1484,"children":1485},"blockquote",{},[1486],{"type":42,"tag":233,"props":1487,"children":1488},{},[1489,1494,1496,1501],{"type":42,"tag":408,"props":1490,"children":1491},{},[1492],{"type":47,"value":1493},"!IMPORTANT",{"type":47,"value":1495}," ",{"type":42,"tag":65,"props":1497,"children":1498},{},[1499],{"type":47,"value":1500},"Patent convention",{"type":47,"value":1502},": In molecular biology patents, SEQ ID NO: 1\nis typically the DNA sequence and SEQ ID NO: 2 is the primary protein. Higher\nSEQ ID NOs are variants or related sequences. Prefer Sequence 2 when selecting\nthe primary protein of interest.",{"type":42,"tag":385,"props":1504,"children":1506},{"id":1505},"_10-organism-length-search",[1507],{"type":47,"value":1508},"10. Organism + Length Search",{"type":42,"tag":233,"props":1510,"children":1511},{},[1512,1514,1520],{"type":47,"value":1513},"Last-resort search when only organism and expected protein length are known.\nUses NCBI's ",{"type":42,"tag":69,"props":1515,"children":1517},{"className":1516},[],[1518],{"type":47,"value":1519},"[SLEN]",{"type":47,"value":1521}," filter for exact length matching.",{"type":42,"tag":397,"props":1523,"children":1525},{"className":399,"code":1524,"language":401,"meta":402,"style":402},"uv run scripts\u002Fncbi_fetch.py organism-length \\\n  --organism \"Arabidopsis thaliana\" --length 1048 --retmax 50 \\\n  -o \u002Ftmp\u002Fresult.json\n",[1526],{"type":42,"tag":69,"props":1527,"children":1528},{"__ignoreMap":402},[1529,1553,1595],{"type":42,"tag":408,"props":1530,"children":1531},{"class":410,"line":411},[1532,1536,1540,1544,1549],{"type":42,"tag":408,"props":1533,"children":1534},{"style":415},[1535],{"type":47,"value":74},{"type":42,"tag":408,"props":1537,"children":1538},{"style":420},[1539],{"type":47,"value":423},{"type":42,"tag":408,"props":1541,"children":1542},{"style":420},[1543],{"type":47,"value":428},{"type":42,"tag":408,"props":1545,"children":1546},{"style":420},[1547],{"type":47,"value":1548}," organism-length",{"type":42,"tag":408,"props":1550,"children":1551},{"style":716},[1552],{"type":47,"value":719},{"type":42,"tag":408,"props":1554,"children":1555},{"class":410,"line":451},[1556,1560,1564,1568,1572,1577,1582,1586,1591],{"type":42,"tag":408,"props":1557,"children":1558},{"style":420},[1559],{"type":47,"value":1300},{"type":42,"tag":408,"props":1561,"children":1562},{"style":700},[1563],{"type":47,"value":703},{"type":42,"tag":408,"props":1565,"children":1566},{"style":420},[1567],{"type":47,"value":1134},{"type":42,"tag":408,"props":1569,"children":1570},{"style":700},[1571],{"type":47,"value":713},{"type":42,"tag":408,"props":1573,"children":1574},{"style":420},[1575],{"type":47,"value":1576}," --length",{"type":42,"tag":408,"props":1578,"children":1579},{"style":627},[1580],{"type":47,"value":1581}," 1048",{"type":42,"tag":408,"props":1583,"children":1584},{"style":420},[1585],{"type":47,"value":738},{"type":42,"tag":408,"props":1587,"children":1588},{"style":627},[1589],{"type":47,"value":1590}," 50",{"type":42,"tag":408,"props":1592,"children":1593},{"style":716},[1594],{"type":47,"value":719},{"type":42,"tag":408,"props":1596,"children":1597},{"class":410,"line":722},[1598,1602],{"type":42,"tag":408,"props":1599,"children":1600},{"style":420},[1601],{"type":47,"value":1426},{"type":42,"tag":408,"props":1603,"children":1604},{"style":420},[1605],{"type":47,"value":448},{"type":42,"tag":1483,"props":1607,"children":1608},{},[1609],{"type":42,"tag":233,"props":1610,"children":1611},{},[1612,1617],{"type":42,"tag":408,"props":1613,"children":1614},{},[1615],{"type":47,"value":1616},"!NOTE",{"type":47,"value":1618}," This often returns multiple candidates. Use the JSON output headers to\nidentify the correct protein.",{"type":42,"tag":50,"props":1620,"children":1622},{"id":1621},"workflow",[1623],{"type":47,"value":1624},"Workflow",{"type":42,"tag":385,"props":1626,"children":1628},{"id":1627},"standard-sequence-retrieval-cascade",[1629],{"type":47,"value":1630},"Standard Sequence Retrieval Cascade",{"type":42,"tag":233,"props":1632,"children":1633},{},[1634],{"type":47,"value":1635},"When trying to find a protein sequence, follow this priority order:",{"type":42,"tag":57,"props":1637,"children":1638},{},[1639,1656,1672,1688,1704,1720,1736],{"type":42,"tag":61,"props":1640,"children":1641},{},[1642,1647,1649,1654],{"type":42,"tag":65,"props":1643,"children":1644},{},[1645],{"type":47,"value":1646},"Direct accession",{"type":47,"value":1648}," — ",{"type":42,"tag":69,"props":1650,"children":1652},{"className":1651},[],[1653],{"type":47,"value":249},{"type":47,"value":1655}," with GenPept\u002FRefSeq accession",{"type":42,"tag":61,"props":1657,"children":1658},{},[1659,1664,1665,1670],{"type":42,"tag":65,"props":1660,"children":1661},{},[1662],{"type":47,"value":1663},"CDS translation",{"type":47,"value":1648},{"type":42,"tag":69,"props":1666,"children":1668},{"className":1667},[],[1669],{"type":47,"value":271},{"type":47,"value":1671}," with nucleotide\u002FCDS accession",{"type":42,"tag":61,"props":1673,"children":1674},{},[1675,1680,1681,1686],{"type":42,"tag":65,"props":1676,"children":1677},{},[1678],{"type":47,"value":1679},"PubMed-linked",{"type":47,"value":1648},{"type":42,"tag":69,"props":1682,"children":1684},{"className":1683},[],[1685],{"type":47,"value":326},{"type":47,"value":1687}," with PMID + gene name",{"type":42,"tag":61,"props":1689,"children":1690},{},[1691,1696,1697,1702],{"type":42,"tag":65,"props":1692,"children":1693},{},[1694],{"type":47,"value":1695},"Locus lookup",{"type":47,"value":1648},{"type":42,"tag":69,"props":1698,"children":1700},{"className":1699},[],[1701],{"type":47,"value":315},{"type":47,"value":1703}," with locus tag + organism",{"type":42,"tag":61,"props":1705,"children":1706},{},[1707,1712,1713,1718],{"type":42,"tag":65,"props":1708,"children":1709},{},[1710],{"type":47,"value":1711},"Gene + organism",{"type":47,"value":1648},{"type":42,"tag":69,"props":1714,"children":1716},{"className":1715},[],[1717],{"type":47,"value":304},{"type":47,"value":1719}," with gene name + organism",{"type":42,"tag":61,"props":1721,"children":1722},{},[1723,1728,1729,1734],{"type":42,"tag":65,"props":1724,"children":1725},{},[1726],{"type":47,"value":1727},"Patent search",{"type":47,"value":1648},{"type":42,"tag":69,"props":1730,"children":1732},{"className":1731},[],[1733],{"type":47,"value":337},{"type":47,"value":1735}," with patent number or keywords",{"type":42,"tag":61,"props":1737,"children":1738},{},[1739,1744,1745,1750],{"type":42,"tag":65,"props":1740,"children":1741},{},[1742],{"type":47,"value":1743},"Organism + length",{"type":47,"value":1648},{"type":42,"tag":69,"props":1746,"children":1748},{"className":1747},[],[1749],{"type":47,"value":348},{"type":47,"value":1751}," as last resort",{"type":42,"tag":385,"props":1753,"children":1755},{"id":1754},"interpreting-results",[1756],{"type":47,"value":1757},"Interpreting Results",{"type":42,"tag":186,"props":1759,"children":1760},{},[1761,1774,1803],{"type":42,"tag":61,"props":1762,"children":1763},{},[1764,1766,1772],{"type":47,"value":1765},"All subcommands return JSON with a ",{"type":42,"tag":69,"props":1767,"children":1769},{"className":1768},[],[1770],{"type":47,"value":1771},"results",{"type":47,"value":1773}," array",{"type":42,"tag":61,"props":1775,"children":1776},{},[1777,1779,1785,1787,1793,1795,1801],{"type":47,"value":1778},"Each result has ",{"type":42,"tag":69,"props":1780,"children":1782},{"className":1781},[],[1783],{"type":47,"value":1784},"sequence",{"type":47,"value":1786}," (AA string), ",{"type":42,"tag":69,"props":1788,"children":1790},{"className":1789},[],[1791],{"type":47,"value":1792},"length",{"type":47,"value":1794},", and ",{"type":42,"tag":69,"props":1796,"children":1798},{"className":1797},[],[1799],{"type":47,"value":1800},"header",{"type":47,"value":1802},"\u002Fmetadata",{"type":42,"tag":61,"props":1804,"children":1805},{},[1806,1808],{"type":47,"value":1807},"When multiple results are returned, select by:\n",{"type":42,"tag":186,"props":1809,"children":1810},{},[1811,1823,1828],{"type":42,"tag":61,"props":1812,"children":1813},{},[1814,1816,1822],{"type":47,"value":1815},"Closest match to expected length (",{"type":42,"tag":69,"props":1817,"children":1819},{"className":1818},[],[1820],{"type":47,"value":1821},"target_length",{"type":47,"value":548},{"type":42,"tag":61,"props":1824,"children":1825},{},[1826],{"type":47,"value":1827},"Header relevance (matching gene name, \"disease resistance\" keywords)",{"type":42,"tag":61,"props":1829,"children":1830},{},[1831],{"type":47,"value":1832},"Source priority (RefSeq > GenPept > patent)",{"type":42,"tag":50,"props":1834,"children":1836},{"id":1835},"reference",[1837],{"type":47,"value":1838},"Reference",{"type":42,"tag":186,"props":1840,"children":1841},{},[1842,1858,1873,1883],{"type":42,"tag":61,"props":1843,"children":1844},{},[1845,1850,1852],{"type":42,"tag":65,"props":1846,"children":1847},{},[1848],{"type":47,"value":1849},"NCBI E-utilities docs",{"type":47,"value":1851},": ",{"type":42,"tag":102,"props":1853,"children":1856},{"href":1854,"rel":1855},"https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Fbooks\u002FNBK25499\u002F",[106],[1857],{"type":47,"value":1854},{"type":42,"tag":61,"props":1859,"children":1860},{},[1861,1866,1867],{"type":42,"tag":65,"props":1862,"children":1863},{},[1864],{"type":47,"value":1865},"Entrez search syntax",{"type":47,"value":1851},{"type":42,"tag":102,"props":1868,"children":1871},{"href":1869,"rel":1870},"https:\u002F\u002Fwww.ncbi.nlm.nih.gov\u002Fbooks\u002FNBK49540\u002F",[106],[1872],{"type":47,"value":1869},{"type":42,"tag":61,"props":1874,"children":1875},{},[1876,1881],{"type":42,"tag":65,"props":1877,"children":1878},{},[1879],{"type":47,"value":1880},"Database list",{"type":47,"value":1882},": protein, nuccore, gene, pubmed, pmc, biosample, etc.",{"type":42,"tag":61,"props":1884,"children":1885},{},[1886,1891,1893],{"type":42,"tag":65,"props":1887,"children":1888},{},[1889],{"type":47,"value":1890},"Common accession formats",{"type":47,"value":1892},":\n",{"type":42,"tag":186,"props":1894,"children":1895},{},[1896,1915,1934,1960,1993],{"type":42,"tag":61,"props":1897,"children":1898},{},[1899,1905,1907,1913],{"type":42,"tag":69,"props":1900,"children":1902},{"className":1901},[],[1903],{"type":47,"value":1904},"XP_",{"type":47,"value":1906}," \u002F ",{"type":42,"tag":69,"props":1908,"children":1910},{"className":1909},[],[1911],{"type":47,"value":1912},"NP_",{"type":47,"value":1914}," — NCBI RefSeq protein",{"type":42,"tag":61,"props":1916,"children":1917},{},[1918,1924,1926,1932],{"type":42,"tag":69,"props":1919,"children":1921},{"className":1920},[],[1922],{"type":47,"value":1923},"AAA",{"type":47,"value":1925}," to ",{"type":42,"tag":69,"props":1927,"children":1929},{"className":1928},[],[1930],{"type":47,"value":1931},"AZZ",{"type":47,"value":1933}," + digits — GenPept (translated GenBank)",{"type":42,"tag":61,"props":1935,"children":1936},{},[1937,1943,1945,1951,1952,1958],{"type":42,"tag":69,"props":1938,"children":1940},{"className":1939},[],[1941],{"type":47,"value":1942},"MK",{"type":47,"value":1944},", ",{"type":42,"tag":69,"props":1946,"children":1948},{"className":1947},[],[1949],{"type":47,"value":1950},"MN",{"type":47,"value":1944},{"type":42,"tag":69,"props":1953,"children":1955},{"className":1954},[],[1956],{"type":47,"value":1957},"HQ",{"type":47,"value":1959},", etc. + digits — GenBank nucleotide",{"type":42,"tag":61,"props":1961,"children":1962},{},[1963,1969,1970,1976,1977,1983,1985,1991],{"type":42,"tag":69,"props":1964,"children":1966},{"className":1965},[],[1967],{"type":47,"value":1968},"ENSG",{"type":47,"value":1944},{"type":42,"tag":69,"props":1971,"children":1973},{"className":1972},[],[1974],{"type":47,"value":1975},"ENST",{"type":47,"value":1944},{"type":42,"tag":69,"props":1978,"children":1980},{"className":1979},[],[1981],{"type":47,"value":1982},"ENSP",{"type":47,"value":1984}," — Ensembl (use ",{"type":42,"tag":69,"props":1986,"children":1988},{"className":1987},[],[1989],{"type":47,"value":1990},"ensembl-database",{"type":47,"value":1992}," skill instead)",{"type":42,"tag":61,"props":1994,"children":1995},{},[1996,2002,2003,2009,2010,2016,2018,2024],{"type":42,"tag":69,"props":1997,"children":1999},{"className":1998},[],[2000],{"type":47,"value":2001},"Q",{"type":47,"value":1944},{"type":42,"tag":69,"props":2004,"children":2006},{"className":2005},[],[2007],{"type":47,"value":2008},"P",{"type":47,"value":1944},{"type":42,"tag":69,"props":2011,"children":2013},{"className":2012},[],[2014],{"type":47,"value":2015},"O",{"type":47,"value":2017}," + digits — UniProt (use ",{"type":42,"tag":69,"props":2019,"children":2021},{"className":2020},[],[2022],{"type":47,"value":2023},"uniprot-database",{"type":47,"value":1992},{"type":42,"tag":2026,"props":2027,"children":2028},"style",{},[2029],{"type":47,"value":2030},"html .light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html.light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html .default .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}html.dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}",{"items":2032,"total":2192},[2033,2046,2061,2081,2093,2108,2123,2134,2146,2161,2171,2181],{"slug":2034,"name":2034,"fn":2035,"description":2036,"org":2037,"tags":2038,"stars":25,"repoUrl":26,"updatedAt":2045},"alphafold-database-fetch-and-analyze","retrieve and analyze AlphaFold protein structures","Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2039,2040,2041,2044],{"name":17,"slug":18,"type":15},{"name":23,"slug":24,"type":15},{"name":2042,"slug":2043,"type":15},"Life Sciences","life-sciences",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:51.827211",{"slug":2047,"name":2047,"fn":2048,"description":2049,"org":2050,"tags":2051,"stars":25,"repoUrl":26,"updatedAt":2060},"alphagenome-single-variant-analysis","analyze genetic variant effects with AlphaGenome","Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue\u002Fcell-type ontologies (UBERON\u002FCL) or analyzing variants in chr:pos:ref>alt format.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2052,2053,2056,2057],{"name":17,"slug":18,"type":15},{"name":2054,"slug":2055,"type":15},"Genetics","genetics",{"name":13,"slug":14,"type":15},{"name":2058,"slug":2059,"type":15},"RNA-seq","rna-seq","2026-07-12T07:51:39.494803",{"slug":2062,"name":2062,"fn":2063,"description":2064,"org":2065,"tags":2066,"stars":25,"repoUrl":26,"updatedAt":2080},"chembl-database","query ChEMBL database for bioactive molecules","Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50\u002FKi values, drug mechanisms, or structure searches.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2067,2070,2073,2076,2079],{"name":2068,"slug":2069,"type":15},"ChEMBL","chembl",{"name":2071,"slug":2072,"type":15},"Chemistry","chemistry",{"name":2074,"slug":2075,"type":15},"Database","database",{"name":2077,"slug":2078,"type":15},"Pharmacology","pharmacology",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:35.544306",{"slug":2082,"name":2082,"fn":2083,"description":2084,"org":2085,"tags":2086,"stars":25,"repoUrl":26,"updatedAt":2092},"clinical-trials-database","query clinical trial data","Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility\u002Finclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient matching.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2087,2090,2091],{"name":2088,"slug":2089,"type":15},"Clinical Trials","clinical-trials",{"name":2042,"slug":2043,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:52:06.846705",{"slug":2094,"name":2094,"fn":2095,"description":2096,"org":2097,"tags":2098,"stars":25,"repoUrl":26,"updatedAt":2107},"clinvar-database","retrieve clinical significance from ClinVar database","Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding \"hard positive\" benchmark controls for human genomic variants.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2099,2102,2103,2106],{"name":2100,"slug":2101,"type":15},"ClinVar","clinvar",{"name":2054,"slug":2055,"type":15},{"name":2104,"slug":2105,"type":15},"Healthcare","healthcare",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:36.86094",{"slug":176,"name":176,"fn":2109,"description":2110,"org":2111,"tags":2112,"stars":25,"repoUrl":26,"updatedAt":2122},"manage and verify API credentials safely","Instructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2113,2116,2119],{"name":2114,"slug":2115,"type":15},"Compliance","compliance",{"name":2117,"slug":2118,"type":15},"Operations","operations",{"name":2120,"slug":2121,"type":15},"Security","security","2026-07-12T07:52:17.355491",{"slug":2124,"name":2124,"fn":2125,"description":2126,"org":2127,"tags":2128,"stars":25,"repoUrl":26,"updatedAt":2133},"dbsnp-database","search genetic variants in dbSNP database","Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings. For an rsID, returns variant type, gene associations, clinical significance, allele frequencies, and genomic coordinates (GRCh38).\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2129,2130,2131,2132],{"name":17,"slug":18,"type":15},{"name":2054,"slug":2055,"type":15},{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:51:33.054229",{"slug":2135,"name":2135,"fn":2136,"description":2137,"org":2138,"tags":2139,"stars":25,"repoUrl":26,"updatedAt":2145},"embl-ebi-ols","search biomedical ontologies in EMBL-EBI OLS","Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP). Use when the user asks to search for terms, retrieve details, navigate hierarchies (parents, children, ancestors), look up properties and individuals, get autocomplete suggestions, or access ontology metadata and statistics.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2140,2141,2144],{"name":17,"slug":18,"type":15},{"name":2142,"slug":2143,"type":15},"Ontology","ontology",{"name":13,"slug":14,"type":15},"2026-07-12T07:51:59.368324",{"slug":2147,"name":2147,"fn":2148,"description":2149,"org":2150,"tags":2151,"stars":25,"repoUrl":26,"updatedAt":2160},"encode-ccres-database","query ENCODE regulatory and experimental data","Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when you want to query regulatory annotations or raw experimental data across human cell types.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2152,2153,2156,2157],{"name":17,"slug":18,"type":15},{"name":2154,"slug":2155,"type":15},"GraphQL","graphql",{"name":13,"slug":14,"type":15},{"name":2158,"slug":2159,"type":15},"REST API","rest-api","2026-07-12T07:52:10.597139",{"slug":1990,"name":1990,"fn":2162,"description":2163,"org":2164,"tags":2165,"stars":25,"repoUrl":26,"updatedAt":2170},"query genomic and protein data from Ensembl","Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2166,2167,2168,2169],{"name":17,"slug":18,"type":15},{"name":2054,"slug":2055,"type":15},{"name":2042,"slug":2043,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:51:41.645835",{"slug":2172,"name":2172,"fn":2173,"description":2174,"org":2175,"tags":2176,"stars":25,"repoUrl":26,"updatedAt":2180},"foldseek-structural-search","perform 3D protein structural searches","Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2177,2178,2179],{"name":17,"slug":18,"type":15},{"name":2042,"slug":2043,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:52:09.354992",{"slug":2182,"name":2182,"fn":2183,"description":2184,"org":2185,"tags":2186,"stars":25,"repoUrl":26,"updatedAt":2191},"gnomad-database","query genetic variant data from gnomAD","Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).\n",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2187,2188,2189,2190],{"name":17,"slug":18,"type":15},{"name":2054,"slug":2055,"type":15},{"name":2042,"slug":2043,"type":15},{"name":13,"slug":14,"type":15},"2026-07-12T07:51:38.213009",38,{"items":2194,"total":2192},[2195,2202,2209,2217,2223,2230,2236],{"slug":2034,"name":2034,"fn":2035,"description":2036,"org":2196,"tags":2197,"stars":25,"repoUrl":26,"updatedAt":2045},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2198,2199,2200,2201],{"name":17,"slug":18,"type":15},{"name":23,"slug":24,"type":15},{"name":2042,"slug":2043,"type":15},{"name":13,"slug":14,"type":15},{"slug":2047,"name":2047,"fn":2048,"description":2049,"org":2203,"tags":2204,"stars":25,"repoUrl":26,"updatedAt":2060},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2205,2206,2207,2208],{"name":17,"slug":18,"type":15},{"name":2054,"slug":2055,"type":15},{"name":13,"slug":14,"type":15},{"name":2058,"slug":2059,"type":15},{"slug":2062,"name":2062,"fn":2063,"description":2064,"org":2210,"tags":2211,"stars":25,"repoUrl":26,"updatedAt":2080},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2212,2213,2214,2215,2216],{"name":2068,"slug":2069,"type":15},{"name":2071,"slug":2072,"type":15},{"name":2074,"slug":2075,"type":15},{"name":2077,"slug":2078,"type":15},{"name":13,"slug":14,"type":15},{"slug":2082,"name":2082,"fn":2083,"description":2084,"org":2218,"tags":2219,"stars":25,"repoUrl":26,"updatedAt":2092},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2220,2221,2222],{"name":2088,"slug":2089,"type":15},{"name":2042,"slug":2043,"type":15},{"name":13,"slug":14,"type":15},{"slug":2094,"name":2094,"fn":2095,"description":2096,"org":2224,"tags":2225,"stars":25,"repoUrl":26,"updatedAt":2107},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2226,2227,2228,2229],{"name":2100,"slug":2101,"type":15},{"name":2054,"slug":2055,"type":15},{"name":2104,"slug":2105,"type":15},{"name":13,"slug":14,"type":15},{"slug":176,"name":176,"fn":2109,"description":2110,"org":2231,"tags":2232,"stars":25,"repoUrl":26,"updatedAt":2122},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2233,2234,2235],{"name":2114,"slug":2115,"type":15},{"name":2117,"slug":2118,"type":15},{"name":2120,"slug":2121,"type":15},{"slug":2124,"name":2124,"fn":2125,"description":2126,"org":2237,"tags":2238,"stars":25,"repoUrl":26,"updatedAt":2133},{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[2239,2240,2241,2242],{"name":17,"slug":18,"type":15},{"name":2054,"slug":2055,"type":15},{"name":20,"slug":21,"type":15},{"name":13,"slug":14,"type":15}]