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parsing script for MSA

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  • parsing script for MSA

    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

  • #2
    BioPerl is what you need.

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