This toolkit is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.

```bibtex theme={null} @article{sayers2022genbank, title={GenBank}, author={Sayers, Eric W and Cavanaugh, Mark and Clark, Karen and Pruitt, Kim D and Schoch, Conrad L and Sherry, Stephen T and Karsch-Mizrachi, Ilene}, journal={Nucleic Acids Research}, volume={50}, number={D1}, pages={D161--D164}, year={2022}, publisher={Oxford University Press}, doi={10.1093/nar/gkab1135} } @article{theuniprotconsortium2025, title={UniProt: the Universal Protein Knowledgebase in 2025}, author={The UniProt Consortium}, journal={Nucleic Acids Research}, volume={53}, number={D1}, pages={D609--D617}, year={2025}, publisher={Oxford University Press}, doi={10.1093/nar/gkae1010} } @article{berman2000pdb, title={The Protein Data Bank}, author={Berman, Helen M and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, T N and Weissig, Helge and Shindyalov, Ilya N and Bourne, Philip E}, journal={Nucleic Acids Research}, volume={28}, number={1}, pages={235--242}, year={2000}, publisher={Oxford University Press}, doi={10.1093/nar/28.1.235} } ```

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### Multi-source Sequence Fetch (`sequence-fetch`) Resolves a list of `SequenceFetchRequest` objects across NCBI Entrez, UniProt, and RCSB PDB, returning per-request fetched sequences, fetched structures, resolved identifiers, warnings, and errors, with run-level counts of successful, warning, and failed requests. #### API Reference

Source One or more retrieval requests. Optional caller-provided request identifier. Gene, protein, or RNA name to resolve. Organism name used for disambiguation. Requested outputs: protein, dna, rna, or structure. UniProt accession override. GenBank accession override. RefSeq accession override. PDB accession override. NCBI Gene ID override. NCBI protein accession override. Transcript accession override. Genomic interval like NC\_000913.3:1-100:+. Extra IDs used for custom routing.

Source Maximum database candidates to evaluate per name-based search. Controls how molecule-type mismatches are handled (e.g. requesting "protein" for a name that looks like an ncRNA gene). `"off"` skips validation entirely; `"warn"` records a warning but continues; `"error"` (default) fails the request. Available options: `off`, `warn`, `error` Optional NCBI API key (lifts rate limit from 3 to 10 requests/second). Defaults to the `NCBI_API_KEY` environment variable; an explicit value passed to the config overrides the env var. Optional contact email. Defaults to the `NCBI_EMAIL` environment variable; an explicit value passed to the config overrides the env var. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Per-request retrieval outcomes. Request identifier used in this result. Original target name. Original organism name. Requested output molecule types. One of success, warning, or failed. Retrieved sequence records. Retrieved structure records. IDs resolved or used during retrieval. Non-fatal warnings. Fatal or partial failure messages.

#### Applications Use this to pull mixed protein, nucleotide, and structure data for many targets in a single call. Resolve a batch of gene symbols plus organisms to reference protein sequences for analysis or design, retrieve coding DNA and transcript RNA alongside the protein for a codon-optimization workflow, or fetch a protein and its linked PDB structures together to seed structure-aware downstream steps. Partial batches are normal. Each request reports its own status, sequences, structures, and errors independently, so one unresolved target does not fail the job. #### Usage Tips * **Provide identifiers whenever possible.** Accession overrides such as `uniprot_id`, `genbank_accession`, or `pdb_id` route directly and are far more reliable than a name-and-organism search, which selects a single top-ranked candidate that may be ambiguous. * **The strand in `genomic_coordinates` changes the returned sequence.** Coordinates are interpreted as 1-indexed, inclusive intervals to match biological residue selection conventions, and an explicit `+` or `-` strand controls whether the forward or reverse-complement sequence is returned. Omitting the strand can yield the wrong-orientation sequence for genes on the minus strand. * **A protein hit does not guarantee a structure exists.** Structure retrieval requires a linked PDB entry. A UniProt or NCBI protein match with no PDB cross-reference produces a not-found error for the `structure` type while the protein sequence still returns. * **`type_check_mode` defaults to `"error"`, the right setting for production.** It rejects obvious molecule-type mismatches early, such as requesting `protein` for a name that looks like a non-coding RNA (ncRNA) gene or for an `NR_` or `XR_` RefSeq transcript. `"warn"` records the mismatch and continues, and `"off"` skips the check entirely. * **`rna_premrna` is inferred, not curated.** It is transcribed from the genomic DNA sequence and includes introns where present, so it is annotation-dependent and not a directly curated transcript.