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biopython

combined

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom molecular-biology pipelines, BLAST automation, structure analysis, and motif analysis. A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.

When to use

• Working with biological sequences (DNA, RNA, or protein)
• Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
• Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
• Running BLAST searches or parsing BLAST results
• Performing sequence alignments (pairwise or multiple sequence alignments)
• Analyzing protein structures from PDB files
• Creating, manipulating, or visualizing phylogenetic trees
• Finding sequence motifs or analyzing motif patterns

When not to use

• Use this skill only when the task clearly matches the scope described above.
• Do not treat the output as a substitute for environment-specific validation, testing, or expert review.
• Stop and ask for clarification if required inputs, permissions, safety boundaries, or success criteria are missing.

Skill page

Conflict

The copies share a common core structure (Overview, When to Use, Core Capabilities, Installation, and module-specific sections) but diverge significantly on versioning, security practices, and scope. The K-Dense-AI copy is the most recent (Biopython 1.88) and includes specific security fixes and environment variable handling for NCBI keys. The aipoch copy provides a unique, complete end-to-end pipeline example with explicit rate-limiting logic (time.sleep) and error handling for missing environment variables. The foryourhealth111 and sickn33 copies are older (Biopython 1.85) and lack these specific operational details. Because the K-Dense copy is outdated in the other repos but the aipoch copy has unique implementation details not present in K-Dense, and the versions conflict, a combined instruction is necessary to capture the best practices from all sources without hiding the version discrepancy.