[Bioperl-l] Aligning two alignments ...

[Sendu Bala]

Stéphane Téletchéa wrote:
> Dear all,
> 
> I'm trying to compare alignments results for small protein sequences to 
> validate my result from another method. In the best option, i would do 
> on two sequences
> 
> - run a clustalw alignment
> - run a blast alignment
> - run a T-Coffee alignment
> - use my own
> 
> And align them all to see easily what is identical, what differs.

You don't want to align the alignments; that makes no sense and you 
can't achieve anything without altering the alignments.

I suppose you actually just want to score the alignments against some 
'ideal' alignment or against one of the others. In which case generate a 
match line/ cigar line/ simply count the number of identical bases 
across different alignment strings.