tooluniverse-sequence-retrieval
Retrieve DNA, RNA, and protein sequences from NCBI and ENA with automatic gene disambiguation and cross-database handling.
- Searches NCBI Nucleotide by organism, gene name, strain, and sequence type; automatically disambiguates genes across species and resolves accession prefixes to the correct database
- Handles RefSeq (NC_, NM_, NP_) and GenBank accessions with intelligent fallback between NCBI and ENA; never attempts ENA queries on RefSeq-only accessions
- Returns detailed sequence profiles including metadata, GC content, annotation summaries, curation levels, and alternative sequences ranked by relevance
- Supports FASTA and GenBank formats with full annotation extraction; provides cross-database references and download instructions for each sequence
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
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