motif

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

NAME

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

VERSION

       Version 0.01

SYNOPSIS

       From a file:

	   revtrans-motif.pl -i motifs.txt

       Using pipes:

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

       Using interactively at the command prompt:

	  $ 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 v5.14.2							    2012-03-02						     BP_REVTRANS-MOTIF(1p)