Biology Biopython
Bioinformatics with Biopython for sequence manipulation, file parsing, BLAST, and...
Install
npx skills add aiming-lab/AutoResearchClaw --skill biology-biopython -g -a claude-code -y- Repository
- aiming-lab/AutoResearchClaw14.8k
- Category
- Engineering
- Updated
- 3mo ago
- License
- MIT
- Context cost
- Lightabout 683 tokens
- Runs scripts
- No, instructions only
What it does
Bioinformatics with Biopython for sequence manipulation, file parsing, BLAST, and phylogenetics. Use when working with DNA/RNA/protein sequences or biological databases.
Biopython Bioinformatics Best Practice
Sequence Manipulation
- Create sequences:
from Bio.Seq import Seq; seq = Seq("ATGCGA") - Complement:
seq.complement(); Reverse complement:seq.reverse_complement() - Transcription:
seq.transcribe()(DNA to RNA) - Translation:
seq.translate()(DNA/RNA to protein) - GC content:
from Bio.SeqUtils import gc_fraction; gc_fraction(seq) - Molecular weight:
from Bio.SeqUtils import molecular_weight
File Parsing (SeqIO)
- Read FASTA:
for rec in SeqIO.parse("file.fasta", "fasta"): ... - Read GenBank:
for rec in SeqIO.parse("file.gb", "genbank"): ... - Read single record:
rec = SeqIO.read("file.fasta", "fasta") - Write sequences:
SeqIO.write(records, "output.fasta", "fasta") - Convert formats:
SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta") - Index large files:
idx = SeqIO.index("large.fasta", "fasta")for random access
BLAST Operations
- Online BLAST:
from Bio.Blast import NCBIWWW; result = NCBIWWW.qblast("blastn", "nt", seq) - Parse results:
from Bio.Blast import NCBIXML; records = NCBIXML.parse(result) - Local BLAST: run via subprocess, parse XML output with NCBIXML
- Always set
Entrez.emailbefore any NCBI access - Filter results by e-value (typically < 1e-5) and coverage
NCBI Database Access (Entrez)
- Always set email:
Entrez.email = "your@email.com" - Search:
handle = Entrez.esearch(db="pubmed", term="query") - Fetch records:
handle = Entrez.efetch(db="nucleotide", id="ID", rettype="fasta") - Use API key for higher rate limits (10 req/s vs 3 req/s)
- Respect NCBI rate limits; add delays between batch requests
