Parse and analyze biological sequences
biopythonskillsetup L2★0
Sheshiyer/skill-clusters ↗What it does
Parse biological sequences and query genomics databases
Best for
Computational biology tasks like sequence alignment, BLAST searches, structure parsing, or phylogenetic analysis.
Inputs
- · FASTA/GenBank/FASTQ files
- · NCBI search terms
- · sequence strings
Outputs
- · parsed SeqRecord objects
- · alignment results
- · BLAST hits
- · phylogenetic trees
Requires
- · Python biopython library
- · NumPy
- · NCBI Entrez API
Preconditions
- · file format matches expected type (FASTA/GenBank)
- · NCBI email configured for Entrez queries
Failure modes
- · rate-limited by NCBI without API key (3 req/s limit)
- · file format mismatch causes parse error
- · sequence not found in database
Trust signals
- · comprehensive module coverage (Seq, Align, Entrez, Blast, PDB, Phylo)
- · supports 20+ biological file formats
- · active development (Biopython 1.85, Jan 2025)