AutoResearchClaw biology-biopython

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