Skip to content

biology-biopython

Category: drafting
Field: —
License: MIT
Updated: 2026-04-23
Stages: paper-drafting

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: idx = SeqIO.index("large.fasta", "fasta") for random access

BLAST Operations

  1. Online BLAST: from Bio.Blast import NCBIWWW; result = NCBIWWW.qblast("blastn", "nt", seq)
  2. Parse results: from Bio.Blast import NCBIXML; records = NCBIXML.parse(result)
  3. Local BLAST: run via subprocess, parse XML output with NCBIXML
  4. Always set Entrez.email before any NCBI access
  5. Filter results by e-value (typically < 1e-5) and coverage

NCBI Database Access (Entrez)

  1. Always set email: Entrez.email = "your@email.com"
  2. Search: handle = Entrez.esearch(db="pubmed", term="query")
  3. Fetch records: handle = Entrez.efetch(db="nucleotide", id="ID", rettype="fasta")
  4. Use API key for higher rate limits (10 req/s vs 3 req/s)
  5. Respect NCBI rate limits; add delays between batch requests

Phylogenetics (Bio.Phylo)

  1. Read trees: from Bio import Phylo; tree = Phylo.read("tree.nwk", "newick")
  2. Draw trees: Phylo.draw(tree) or Phylo.draw_ascii(tree)
  3. Supported formats: newick, nexus, phyloxml
  4. Traverse clades: for clade in tree.find_clades(): ...
  5. Calculate distances: tree.distance(clade1, clade2)

Structure Analysis (Bio.PDB)

  1. Parse PDB: parser = PDBParser(); structure = parser.get_structure("id", "file.pdb")
  2. Hierarchy: Structure > Model > Chain > Residue > Atom
  3. Get atoms: iterate through structure.get_atoms()
  4. Calculate distances: use atom coordinate vectors
  5. For mmCIF files: use MMCIFParser() instead of PDBParser()

Common Pitfalls

  1. Always handle SeqIO.parse as an iterator — it exhausts after one pass
  2. Check sequence alphabet compatibility before operations
  3. Large files: use SeqIO.index() not SeqIO.to_dict() to avoid memory issues
  4. Set proper timeout for remote BLAST queries (can take minutes)
  5. Validate parsed data — missing annotations are common in public databases