Evaluate a multiple sequence alignment

Question

I am using python to doing multiple sequence alignment.for evaluate the alignment I use Weighted sum of pairs score (WSP) for three sequences seq1, seq2 and seq3, as we know the score is calculate as follows: first calculate the score of (seq1,seq2), and score of(seq1,seq3) and score of (seq2,seq3)

WSP=score(seq1,seq2)+score(seq1,seq3)+score(seq2,seq3)

python code:

def wsp():
        w=1
        dis=sum_distance(seq1,seq2,seq3)
        wsp=w*dis
        return wsp

now, I want to use a fasta file which contains many sequences.how can I calculate the WSP score for all sequences in a fasta file.

where sum_distance is a function to calculate distances between sequences

Do you want to get all possible triples of sequences, and compute the WSP of each triple? — inspectorG4dget
Have you looked into using Biopython? I haven't checked if it includes WSP or sum of distances, but I wouldn't be surprised if it did. It includes all sorts of tools for working with and aligning sequences, and is much easier than coding everything yourself. — MattDMo
for example for the three sequences seq1='AG-GT' seq2='AG-GT and seq3='ACT-T' the WSP function for the three sequences score gives 8. — user3216969

scezar scezar · Accepted Answer · 2014-12-23T23:36:12

The simplest way is to run sum_distance function over each pair of sequences in your file:

total_distance = 0  
with open('yourfile.fa', 'r') as sequences_list_1:
    for key_1, seq_1 in enumerate(sequences_list_1):
        with open('yourfile.fa', 'r') as sequences_list_2:
            for key_2, seq_2 in enumerate(sequences_list_2):
                if key_1 < key_2:
                    total_distance += sum_distance(seq_1, seq_2)

Evaluate a multiple sequence alignment

1 Answers