biopython
Category: life-sciences · License: Biopython License Agreement · Version: 1.3
Tags: sequence analysis, bioinformatics, BLAST, NCBI, phylogenetics, Python
When to use it
Provides Biopython (Bio.Seq, Bio.SeqIO, Bio.Align, Bio.Entrez, Bio.Blast, Bio.PDB, Bio.Phylo, Bio.motifs, Bio.SeqUtils, Bio.Restriction) for sequence handling, file parsing, NCBI access, BLAST, structures, and phylogenetic trees in Python. Reads, writes, and converts FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and NEXUS files. Use when manipulating or translating DNA, RNA, or protein sequences, converting sequence file formats, fetching records from NCBI via Entrez, running or parsing BLAST searches, doing pairwise or multiple sequence alignment, analyzing PDB structures, or building and editing phylogenetic trees. For quick lookups use gget; for multi-service integration use bioservices.Example requests
Ask your agent in plain language, for example:- “How do I reverse-complement a DNA string and translate it in Python?”
- “I have a GenBank file called plasmid_pUC19.gb and need a FASTA of just the CDS translations for each annotated gene, plus a GFF-free list of locus_tags. I’m getting ‘ValueError: Sequence content is undefined’ on some features when I call feature.extract(record.seq). What’s going on and how do I fix it?”
- “I’ve got about 40 accession numbers for the cytochrome b gene from different mammals. I want to pull them from NCBI, line them up, and draw a tree showing how the species relate to each other, all in one Python script.”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.