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Man Pages


Manual Reference Pages  -  BP_REVTRANS-MOTIF.PL (1)

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NAME

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

CONTENTS

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:
<B>[...]B> : Redundant position. A position in which more than one residue is allowed. Example:



    [TS]YW[RKSD]
     ^^    ^^^^



<B>[^...]B> : Negated position. A position in which any residue is allowed, saved for those between brackets. Example:



    [^PW]MK[LAE]
      ^^



<B>(...){n,m,...}B> : Repeated motif. A motif that is repeated <B>nB> or <B>mB> 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.

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perl v5.20.3 BP_REVTRANS-MOTIF (1) 2016-04-05

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