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pairwise alignment for multiple sequences in a file

I have about 10 protein/DNA sequences in a file in FASTA format and would like to do a pairwise alignment for all possible combinations in this file.

Example: 

 Seq1 vs Seq2
 Seq1 vs Seq3
 Seq1 vs Seq4 and so on.

Are there tools that can perform this?

alignment pairwise fasta
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updated by st.ph.n st.ph.n • written by biobudhan • biobudhan

1 answer

You can use itertools in python, and pairwise2 from BioPython. Itertools.combinations will create the combinations of sequences you need for each alignment.

#!/usr/bin/env python
import itertools, sys
from Bio import SeqIO, pairwise2

fasta = sys.argv[1]
with open(fasta, 'r') as f:
    seqs = []
    for line in f:
        if not line.startswith('>'):
            seqs.append(line.strip())

combos = itertools.combinations(seqs, 2)

for k,v in combos:
    aln = pairwise2.align.localxx(k,v)
    print pairwise2.format_alignment(*aln[0])

Save as aln.py; run as python aln.py your_fasta_file.fasta

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written by st.ph.n st.ph.n

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