NAME

       bp_revtrans-motif - Reverse translate a Profam-like protein motif

VERSION

       Version 0.01

SYNOPSIS

       From a file:

           bp_revtrans-motif.pl -i motifs.txt

       Using pipes:

          bp_revtrans-motif.pl < motifs.txt > output.txt

       Using interactively at the command prompt:

          $ bp_revtrans-motif.pl
          MAAEEL[VIKP]
          1.   ATGGCNGCNGARGARYTNVHN
          [^P]H(IW){2,3}
          2.   NDNCAY(ATHTGG){2,3}

DESCRIPTION

       This script takes a protein motif as input and returns a degenerate oligonucleotide
       sequence corresponding to it. The main reason for doing this is to design degenerate
       primers that amplify a given sequence pattern.

       The input motif consists of a string of one-letter residues, with any of the following
       syntactic elements:

       [...] : Redundant position.
           A position in which more than one residue is allowed. Example:

               [TS]YW[RKSD]
                ^^    ^^^^

       [^...] : Negated position.
           A position in which any residue is allowed, saved for those between brackets. Example:

               [^PW]MK[LAE]
                 ^^

       (...){n,m,...} : Repeated motif.
           A motif that is repeated n or m times. It can have any of the previous syntactic
           elements. Example:

               A[SN]C(TXX){2,4,8}
                      ^^^

       The allowed letters are those that correspond to the 20 natural aminoacids, plus:

           B = N + D
           Z = Q + E
           X = All

OPTIONS

   -i input-file:
       A file with a list of motifs to reverse translate.

   -h
       Display this help message.

AUTHOR

       Bruno Vecchi, "vecchi.b at gmail.com"

BUGS

       Please report any bugs or feature requests to "vecchi.b at gmail.com"

COPYRIGHT & LICENSE

       Copyright 2009 Bruno Vecchi, all rights reserved.

       This program is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.