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NCBI Datasets

Programmatic access to NCBI genomes and sequences

NCBI is the US hub for biological sequence data — GenBank, RefSeq, SRA, PubMed and more. NCBI Datasets modernizes access with a command-line tool and REST API for bulk retrieval.

Example

1datasets download genome accession GCF_000001405.40 --include genome,gff3

Pair with Entrez utilities for literature and cross-database queries.

Related tools

Liftoff.bio illustration — cat databases
Free

Public Databases

Ensembl

Genome annotation and comparative genomics

Web appREST APIDataset
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Free

Public Databases

UniProt

The universal protein knowledgebase

Web appREST APIDataset
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Open source

Libraries & SDKs

Biopython

The foundational Python library for computational biology

Python library