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

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

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

       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 v5.32.1                                       2021-08-15                              BP_REVTRANS-MOTIF(1p)

       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

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

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

   -h
       Display this help message.

       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}

       Version 0.01