How to get all possible alignments from MAFFT or another global aligner

Question

[Elephantdumbo]

Hey guys I have two sequences

> sequence1
 TAGTAGTAG
> Sequence2 
TAG

MAFFT aligns it as

TAGTAGTAG

------TAG

I want it to also output

TAGTAGTAG

TAG------

and

TAGTAGTAG

---TAG---

Does anyone knows how to do that ?

Thank you

Answer 1

[Mensur Dlakic]

The first two alignments are equivalent in terms of score, but the third one isn't because the gap is opened twice.

Alignment programs are geared towards finding an optimal alignment rather than finding all alignments. It really is wasteful to output all the possible sub-optimal alignments. It may not seem so for your toy example, but for 500 sequences of average length 300 and with some repeats in them, this would be a huge output of suboptimal alignments. It is difficult enough (and sometimes slow enough) to output the best alignment only, let alone to do so for thousands of suboptimal results.

[Mensur Dlakic]

To actually answer your question, if you are willing to work a bit: there is a toy global alignment program written by Sean Eddy in the supplement of this paper:

https://www.nature.com/articles/nbt0704-909

You should be able to modify it such that it outputs alignments that fit your need.

[Elephantdumbo]

Hey Thanks for your response !

I am only interested in pairwise alignment. I will not be aligning 500 sequences. Thanks for the paper. I think it will be helpful

I am interested in sub-optimal alignment because I am trying to model repeat clusters misaligning. If you have any advice regarding that it will be really appreciated.

Thank you so much