I do not know what happend but the text didn't get formatted correctly on the list. But this is how the out put should really have been:
a g a t a g a t c g c a t c g a - - - - - - dog a c g c t t c g a t a c g c t a g c t t a - cat a g a t a t a c g g g t t - - - - - - - - - mouse
That is, I want the edited sequence data and the name on the same line.
I'd hate to mess with your DNA (but just in case -- I, for one, welcome our new super dog-cat-mouse mutant overlords) but I'll post two links you may find interesting (if you don't already know them, that is).
First, you might take a look at the bioperl project: http://bioperl.org/ There's a mailing list you may find very useful, bioperl-l at bioperl.org: http://www.bioperl.org/MailList.shtml
There's also a book, Beginning Perl for Bioinformatics written by James Tisdall: http://www.oreilly.com/catalog/begperlbio/
I wish you good luck with your creations.
-zsdc.
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