Sequence Alignment

Tools for aligning biological sequences.

Pairwise Alignment

from Bio import pairwise2
from Bio.pairwise2 import format_alignment

seq1 = "ACCGGT"
seq2 = "ACGT"

# Global alignment (Needleman-Wunsch)
alignments = pairwise2.align.globalxx(seq1, seq2)
print(format_alignment(*alignments[0]))

# Local alignment (Smith-Waterman)
alignments = pairwise2.align.localxx(seq1, seq2)

# With scoring parameters
alignments = pairwise2.align.globalms(seq1, seq2,
                                       match=2,
                                       mismatch=-1,
                                       open=-0.5,
                                       extend=-0.1)

Substitution Matrices

from Bio.Align import substitution_matrices

# Load BLOSUM62
blosum62 = substitution_matrices.load("BLOSUM62")

# Access scores
score = blosum62["A", "A"]  # Match score
score = blosum62["A", "R"]  # Mismatch score

Multiple Sequence Alignment

from Bio.Align.Applications import MuscleCommandline
from Bio import AlignIO

# Run MUSCLE alignment
muscle_cline = MuscleCommandline(input="sequences.fasta",
                                  out="aligned.fasta")
muscle_cline()

# Read alignment
alignment = AlignIO.read("aligned.fasta", "fasta")
print(f"Alignment length: {alignment.get_alignment_length()}")
print(f"Number of sequences: {len(alignment)}")

# Calculate conservation
from Bio.Align import AlignInfo
summary = AlignInfo.SummaryInfo(alignment)
consensus = summary.dumb_consensus()