Parse and write FASTA, GenBank, FASTQ, and PDB files with Biopython.
npx skills add https://github.com/jackspace/ClaudeSkillz --skill biopython
Please help me install this Agent Skill. Skill: biopython Source: https://github.com/jackspace/ClaudeSkillz/tree/main/skills/scientific-pkg-biopython Command: npx skills add https://github.com/jackspace/ClaudeSkillz --skill biopython
Biopython provides a comprehensive Python toolkit for molecular biology tasks, from sequence handling to BLAST and phylogenetics.
Install Biopython and perform a simple SeqIO parse example.
High-intent search queries and answers about installing and using this skill.
Biopython's SeqIO module parses FASTA, GenBank, FASTQ, and PDB files directly. Load sequences with SeqIO.parse(), then access individual records, their sequences, and annotations programmatically for downstream analysis.
Yes. Biopython's Bio.Blast module executes BLAST queries, and Bio.Entrez accesses GenBank and PubMed data directly. Set Entrez.email first, then retrieve sequences and run comparisons within your Python workflow.
Biopython's Bio.Align handles sequence alignments, and Bio.Phylo constructs and analyzes phylogenetic trees. Both modules work with standard bioinformatics formats and integrate with sequence data from SeqIO or Entrez queries.
Biopython's Bio.PDB module reads PDB files and provides tools to parse atomic coordinates, residues, and chains. Extract structural features and perform geometric analysis programmatically for structure-function studies.
Biopython requires Python 3 and NumPy; bioinformatics background is helpful but not required. The modular design lets you start with simple tasks like file parsing and progressively tackle BLAST, alignments, and phylogenetics.
Entrez enforces rate limits on unauthenticated requests; limits increase with an API key. Biopython supports optional API keys to enable higher-throughput GenBank and PubMed queries for large-scale data retrieval.
shushuznParse and convert FASTA, GenBank, FASTQ, and PDB files using Biopython modules.
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