BioPython

BioPython provides tools for biological computation in Python.

Core Modules

from Bio import SeqIO          # Sequence I/O
from Bio.Seq import Seq        # Sequence objects
from Bio.SeqRecord import SeqRecord
from Bio import Entrez         # NCBI database access
from Bio import AlignIO        # Alignment I/O
from Bio.Blast import NCBIWWW  # BLAST searches

Reading Sequences

# Parse FASTA file
for record in SeqIO.parse("sequences.fasta", "fasta"):
    print(f"ID: {record.id}")
    print(f"Sequence: {record.seq}")
    print(f"Length: {len(record.seq)}")

# Parse GenBank file
for record in SeqIO.parse("sequence.gb", "genbank"):
    print(f"Features: {len(record.features)}")

Sequence Operations

from Bio.Seq import Seq

seq = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")

# Transcription and translation
mrna = seq.transcribe()
protein = seq.translate()

# Complement and reverse complement
complement = seq.complement()
rev_complement = seq.reverse_complement()

Writing Sequences

records = [
    SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF"),
              id="seq1", description="Example protein")
]
SeqIO.write(records, "output.fasta", "fasta")