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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 v5.32.0			  2019-12-07		  BP_REVTRANS-MOTIF(1)

NAME | VERSION | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | BUGS | COPYRIGHT & LICENSE

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