biopython

Parse FASTA, FASTQ, GenBank, and PDB files for biological sequence analysis.

19|2|Updated Jan 31, 2026

Search Tags:#bioinformatics #protein structure #genomics #sequence analysis #ncbi #phylogenetics

Ready to run

npx skills add https://github.com/tondevrel/scientific-agent-skills --skill biopython-tondevrel

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: biopython
Source: https://github.com/tondevrel/scientific-agent-skills/tree/main/skills/biopython
Command: npx skills add https://github.com/tondevrel/scientific-agent-skills --skill biopython-tondevrel

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides comprehensive tools and guidance for computational biology and bioinformatics tasks, streamlining complex biological data analysis.

Core Features & Use Cases

Sequence Analysis: Parse, manipulate, and analyze DNA, RNA, and protein sequences.
File I/O: Read and write common bioinformatics file formats (FASTA, FASTQ, GenBank, PDB).
Alignment & BLAST: Perform sequence alignments and run BLAST searches against biological databases.
Structure Analysis: Analyze protein structures from PDB files.
Phylogenetic Trees: Build and analyze evolutionary relationships.
NCBI Database Access: Interact with NCBI databases like Entrez.
Use Case: Analyze a newly sequenced DNA fragment by parsing its FASTA file, translating it into protein, and performing a BLAST search against the NCBI nr database to identify potential gene functions.

Quick Start

Use the biopython skill to parse the file 'sequences.fasta' and print the ID and length of each sequence.

Frequently Asked Questions about biopython

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I parse and analyze a FASTA file for sequence analysis?▼

To perform sequence analysis on a FASTA file, you can use this toolkit to parse the file and extract information like sequence IDs and lengths. It utilizes the SeqIO module to read, manipulate, and analyze DNA, RNA, and protein sequences.

What is the best way to run a BLAST search against the NCBI database?▼

The best way to run a BLAST search against the NCBI database is using the NCBIWWW module to query biological databases directly. This allows you to identify potential gene functions by comparing your biological sequences against the NCBI nr database.

Can I analyze protein structures from PDB files?▼

Yes, you can analyze protein structures from PDB files. The toolkit includes the PDBParser module specifically for reading PDB file formats and facilitating the structural analysis of biological molecules.

How do I build a phylogenetic tree from biological sequences?▼

You can build a phylogenetic tree by first aligning your biological sequences using the pairwise2 module for sequence alignment. The toolkit then facilitates the construction and analysis of evolutionary relationships based on those aligned sequences.

Does this toolkit support reading and writing FASTQ and GenBank formats?▼

Yes, this toolkit fully supports reading and writing common bioinformatics file formats including FASTQ and GenBank. The SeqIO module handles File I/O operations, enabling seamless parsing and generation of these standard biological data files.