lunar (1) bp_revtrans-motif.1p.gz

Provided by: bioperl_1.7.8-1_all bug

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 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.