| name | tooluniverse-sequence-retrieval |
| description | Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation. Quality hierarchy: RefSeq (NM_/NP_) > RefSeq predicted (XM_/XP_) > GenBank submissions. Use for fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval, and curated-vs-raw-submission preference. |
Biological Sequence Retrieval
Retrieve DNA, RNA, and protein sequences with proper disambiguation and cross-database handling.
IMPORTANT: Always use English terms in tool calls. Only try original-language terms as fallback. Respond in the user's language.
LOOK UP DON'T GUESS: Never assume accession numbers or sequence versions. Always retrieve and verify from NCBI or ENA.
Domain Reasoning
Sequence quality hierarchy: RefSeq (NM_/NP_ = curated) > RefSeq predicted (XM_/XP_) > GenBank (submitted). Prefer the MANE Select transcript for human canonical isoforms. Check version numbers -- annotations improve across versions.
Workflow
Phase 0: Clarify (if needed) → Phase 1: Disambiguate Gene/Organism → Phase 2: Search & Retrieve → Phase 3: Report
Phase 0: Clarification (When Needed)
Ask ONLY if: gene exists in multiple organisms, sequence type unclear, or strain matters.
Skip for: specific accessions, clear organism+gene combos, complete genome requests with organism.
Phase 1: Gene/Organism Disambiguation
Accession Type Decision Tree
| Prefix | Type | Use With |
|---|
| NC_/NM_/NR_/NP_/XM_ | RefSeq | NCBI only |
| U*/M*/K*/X*/CP*/NZ_ | GenBank | NCBI or ENA |
| EMBL format | EMBL | ENA preferred |
CRITICAL: Never try ENA tools with RefSeq accessions -- they return 404.
