If you can implement the Needeman-Wunsch dynamic algorithm you could get the gaps but not to reinvent the wheel, there is a CPAN module Algorithm::NeedlemanWunsch for that.

As for the substitutions, I am not clear on how strict your criteria are and the type of sequences you have but maybe FindMod at ExPasy can be a choice...

BLASTing would conduct local similarity searches which are not the OP's goal..

Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.

In reply to Re: Sequence alignment by biohisham
in thread Sequence alignment by nicholaspr

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