How to compute multiple sequence alignment for text strings

Question

I'm writing a program which has to compute a multiple sequence alignment of a set of strings. I was thinking of doing this in Python, but I could use an external piece of software or another language if that's more practical. The data is not particularly big, I do not have strong performance requirements and I can tolerate approximations (ie. I just need to find a good enough alignment). The only problem is that the strings are regular strings (ie. UTF-8 strings potentially with newlines that should be treated as a regular character); they aren't DNA sequences or protein sequences.

I can find tons of tools and information for the usual cases in bioinformatics with specific complicated file formats and a host of features I don't need, but it is unexpectly hard to find software, libraries or example code for the simple case of strings. I could probably reimplement any one of the many algorithms for this problem or encode my string as DNA, but there must be a better way. Do you know of any solutions?

Thanks!

Answer 1

• The easiest way to align multiple sequences is to do a number of pairwise alignments.

First get pairwise similarity scores for each pair and store those scores. This is the most expensive part of the process. Choose the pair that has the best similarity score and do that alignment. Now pick the sequence which aligned best to one of the sequences in the set of aligned sequences, and align it to the aligned set, based on that pairwise alignment. Repeat until all sequences are in.

When you are aligning a sequence to the aligned sequences, (based on a pairwise alignment), when you insert a gap in the sequence that is already in the set, you insert gaps in the same place in all sequences in the aligned set.

Lafrasu has suggested the SequneceMatcher() algorithm to use for pairwise alignment of UTF-8 strings. What I've described gives you a fairly painless, reasonably decent way to extend that to multiple sequences.

In case you are interested, it is equivalent to building up small sets of aligned sequences and aligning them on their best pair. It gives exactly the same result, but it is a simpler implementation.

Answer 2

Are you looking for something quick and dirty, as in the following?

from difflib import SequenceMatcher  a = "dsa jld lal" b = "dsajld kll" c = "dsc jle kal" d = "dsd jlekal"  ss = [a,b,c,d]  s = SequenceMatcher()  for i in range(len(ss)):     x = ss[i]     s.set_seq1(x)     for j in range(i+1,len(ss)):          y = ss[j]         s.set_seq2(y)          print         print s.ratio()         print s.get_matching_blocks()