biopython

name: biopython description: "Molecular biology toolkit. Use for FASTA parsing, sequence analysis, and translation."

BioPython — Molecular Biology Toolkit

When to Use

• Parsing FASTA sequence files
• Analyzing protein or nucleotide sequences
• Computing sequence composition and molecular weight
• Translating DNA to protein
• Working with sequence alignments

Available Tools

• parse_fasta(path) — Read FASTA file, return sequence metadata
• analyze_sequence(sequence, seq_type) — Composition, MW, stats
• analyze_sequence(sequence, seq_type="DNA", translate=true) — Translate DNA→protein

Amino Acid Properties

• Hydrophobic: A, V, L, I, M, F, W, P
• Polar: S, T, N, Q, Y, C
• Positive: K, R, H
• Negative: D, E
• Special: G (flexible), P (rigid)

Common Sequence Analysis Tasks

1. Check sequence length and composition
2. Identify signal peptides (N-terminal Met + hydrophobic stretch)
3. Find potential glycosylation sites (N-X-S/T)
4. Calculate theoretical pI and MW