biopython
Provides Biopython workflows for sequence manipulation, file parsing
by k-dense-aiFree
Description
biopython is an agent skill that provides Biopython workflows for computational molecular biology in Python. Biopython is a set of freely available tools that cover sequence manipulation, file input and output, database access, structural bioinformatics and phylogenetics. The skill is for tasks such as parsing and writing FASTA, GenBank and PDB files, working with sequences, and making programmatic requests to NCBI and PubMed through Bio.Entrez. Its examples target Biopython 1.88, released on 6 August 2026, and were tested on Python 3.13. Biopython requires Python 3.10 or newer and NumPy, and the skill notes that Python 3.10 support is deprecated. It advises upgrading to 1.88 for a security fix in the Bio.Nexus parser, in addition to an earlier Entrez XML fix in 1.87. The skill records which local checks were run and which external-service limits apply. Examples that need your own files or external programs are illustrative unless the review says they were exercised. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs.…
Highlights
- Sequence manipulation and file parsing
- FASTA, GenBank and PDB support
- Phylogenetics and structural bioinformatics
- NCBI and PubMed access through Bio.Entrez
- Targets Biopython 1.88 on Python 3.13
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biopython FAQ
What can Biopython do?
Sequence manipulation, reading and writing sequence and structure files, database access, phylogenetics and other bioinformatics tasks.
Can it query NCBI and PubMed?
Yes. The skill covers programmatic access through Bio.Entrez.
What does it require?
Python 3.10 or newer and NumPy. The skill notes Python 3.10 support is deprecated, and it recommends Biopython 1.88.
Were the examples tested?
The skill says its examples target Biopython 1.88 and were tested on Python 3.13. Examples that need your own files or external programs are illustrative unless listed as exercised.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill biopython.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best biopython alternatives?
Popular alternatives to biopython include gget, gget and gtars. See all biopython alternatives