parsing script for MSA

[roro]

Hi,

I need help writing a script in Perl to parse the following type of sequence alignment from a FASTA file, residue by residue to compare each position:

MVATFNPAVGSHVWVEDPDEAWLDGEVVEINGDQIKVLCASGKQVVVKDSNIYPKDVEAP
MAASELYTKFARVWIPDPEEVWKSAELLKDYKPGDKVLLLHLEEGKDLEYHLDPKTKELP

Can anyone help?

Thanks

[Shannon Blonk]

BioPerl is what you need.