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ncbi_sequence

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NCBI E-utilities for biological sequences — fetch protein/nucleotide FASTA by accession, run BLAST, translate CDS to protein, search NCBI Protein by gene+organism. Use when the user provides an NCBI accession (NP_, XP_, NM_, NR_, etc.), asks for a sequence by gene name + species, or needs to translate a coding sequence. Don't use for ClinVar variants (use ncbi_clinvar) or gene metadata lookup (use ncbi_gene).

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NCBI Sequence Tools

Overview

Wraps NCBI E-utilities (efetch, esearch) for sequence-centric workflows. Honors NCBI_API_KEY env var to raise the QPS limit from 3 → 10. Set USER_EMAIL env var to identify yourself to NCBI as a good citizen.

Project Tools (VenusFactory2)

ToolArgsReturnsDescription
download_ncbi_sequencencbi_id, out_dir, db (default protein)rich JSON envelope; FASTA fileFetch a single sequence by accession from protein or nuccore.
download_ncbi_metadatancbi_id, out_path, dbrich JSON envelope; metadata JSONFetch GenBank-style metadata for an accession.
download_ncbi_blast(see existing schema)rich JSON envelopeNCBI-hosted BLAST. Prefer download_mmseqs2_homologs_by_sequence (faster) or download_blast_homologs_by_sequence (EBI mirror) for protein-protein searches.
translate_ncbi_cds_to_proteinaccession (nuccore, e.g. NM_000518 for HBB mRNA), out_dir, target_length (default 0 = longest), timeoutrich JSON envelope; FASTA at <out_dir>/<accession>_protein.fasta; biological_metadata.method="fasta_cds_aa"Use efetch(rettype=fasta_cds_aa) to get the CDS-translated protein, pick the translation closest to target_length (or longest).
search_ncbi_protein_by_gene_and_organismgene (e.g. TP53), organism ("Homo sapiens"), out_dir, target_length (default 0 = no length filter; non-zero filters to ±25 aa window), retmax (default 10), timeoutrich JSON envelope; multi-FASTA + <stem>.json summary; biological_metadata.summary_path for the per-hit JSONSearch NCBI Protein DB with <gene>[Gene Name] AND <organism>[Organism], fetch all hits as multi-FASTA.

Workflow: "Get the protein sequence for gene X in species Y"

  1. Try search_ncbi_protein_by_gene_and_organism first — if it finds 1-5 hits, pick the canonical one.
  2. If you know the mRNA accession (e.g. from a Gene record), use translate_ncbi_cds_to_protein for the canonical CDS-derived protein (no ambiguity from isoforms).
  3. Fallback: keyword search via download_ncbi_metadata to find an accession, then download_ncbi_sequence.

Workflow: "Translate this mRNA to protein"

  • Direct: translate_ncbi_cds_to_protein(accession=..., target_length=expected_aa_count). The tool uses NCBI's pre-translated CDS protein when available — no client-side translation needed, no codon-table issues.

Common Mistakes

  • Confusing protein and nuccore DBs: protein accessions (NP_, XP_, AAA-style) go to db=protein; mRNA/genomic (NM_, NC_, etc.) go to db=nuccore. translate_ncbi_cds_to_protein always uses nuccore internally.
  • Mismatched gene+organism: NCBI is strict; TP53 AND Homo sapiens works, tp53 AND human may not.
  • Forgetting NCBI_API_KEY: at 3 QPS you'll hit rate limits with batch operations. Set the env var to bump to 10 QPS.
  • target_length too narrow: search_ncbi_protein_by_gene_and_organism applies ±25 aa filter; if your target_length is uncertain, pass 0 and pick from results.

References