biology-biopython

name	biology-biopython
description	Bioinformatics with Biopython for sequence manipulation, file parsing, BLAST, and phylogenetics. Use when working with DNA/RNA/protein sequences or biological databases.
metadata	{"category":"domain","trigger-keywords":"sequence,FASTA,genome,protein,BLAST,phylogenetic,biopython,bioinformatics,gene,DNA,RNA","applicable-stages":"9,10,12","priority":"4","version":"1.0","author":"researchclaw","references":"adapted from K-Dense-AI/claude-scientific-skills"}

Biopython Bioinformatics Best Practice

Sequence Manipulation

1. Create sequences: from Bio.Seq import Seq; seq = Seq("ATGCGA")
2. Complement: seq.complement(); Reverse complement: seq.reverse_complement()
3. Transcription: seq.transcribe() (DNA to RNA)
4. Translation: seq.translate() (DNA/RNA to protein)
5. GC content: from Bio.SeqUtils import gc_fraction; gc_fraction(seq)
6. Molecular weight: from Bio.SeqUtils import molecular_weight

File Parsing (SeqIO)

1. Read FASTA: for rec in SeqIO.parse("file.fasta", "fasta"): ...
2. Read GenBank: for rec in SeqIO.parse("file.gb", "genbank"): ...
3. Read single record: rec = SeqIO.read("file.fasta", "fasta")
4. Write sequences: SeqIO.write(records, "output.fasta", "fasta")
5. Convert formats: SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta")
6. Index large files: for random access