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bp_revtrans-motif.pl

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 1 (Commandes utilisateur)

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 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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