Multiple sequence alignment analysis

[biobudhan]

Hi all,
I need some help w.r.t Multiple sequence alignment analysis. Can anyone let me know how to calculate the number of insertions and deletions in MSA?

Is there any tool for doing this?

Thanks,
-Suda

[*#1*]

Normally NGS aligners would produce some sort of .gff or .bed file that would contain information about indels, so you would simply need to grep for "del" or "ins" or whichever is the tag. So, you may see if you can generate the alignment using one of the reference mappers you may have. If you do not have a reference, you can use the consensus of the MSA you already have as a reference, and map reads to it. On the other hand, if you can export your alignment into a genome browser, some browsers may have an option of producing the conflict annotations that you can then save as .gff, .bed, etc. Try IGV, IGB, CLC Bio, and other viewers. I have not done that all above myself, but if I had to, I'd proceed along the lines with what I described above first.