biopython

Biopython's SeqIO module reads sequence files in FASTA, GenBank, FASTQ, and other formats. Use Bio.SeqIO.parse() to iterate over sequences or Bio.SeqIO.read() for single files, then access sequence data, annotations, and features programmatically.

Yes, Biopython's Bio.Entrez module provides programmatic access to NCBI databases including PubMed, GenBank, Protein, and Gene. Set Entrez.email and use efetch, esearch, and epost functions to retrieve and parse biological records automatically.

Bio.Blast lets you run local or remote BLAST queries and parse output in XML format. Submit sequences, retrieve results, and extract alignment data, scores, and hit information without manual parsing.

Biopython's Bio.PDB module reads PDB and mmCIF structure files, providing access to atoms, residues, chains, and models. Analyze coordinates, compute distances, and extract structural features for computational structural bioinformatics tasks.

Bio.Seq handles sequence translation between DNA, RNA, and protein alphabets with built-in codon tables. While Biopython parses alignment formats, it integrates with external tools for alignment generation and provides motif analysis across sequences.

Biopython requires Python 3 and NumPy as a core dependency. Installation via pip pulls required packages; optional dependencies extend functionality for phylogenetics, structural analysis, and other specialized subpackages.