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BP_REVTRANS-MOTIF(1)  User Contributed Perl Documentation BP_REVTRANS-MOTIF(1)

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.

perl v5.20.2                      2015-09-15              BP_REVTRANS-MOTIF(1)