Christopher Fields > BioPerl-1.6.923 > bp_revtrans-motif

Download:
BioPerl-1.6.923.tar.gz

Annotate this POD

CPAN RT

New  9
Open  4
View/Report Bugs
Source   Latest Release: BioPerl-1.6.924

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.

syntax highlighting: