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.\" ========================================================================
.\"
.IX Title "BP_REVTRANS-MOTIF 1p"
.TH BP_REVTRANS-MOTIF 1p "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
bp_revtrans\-motif \- Reverse translate a Profam\-like protein motif
.SH "VERSION"
.IX Header "VERSION"
Version 0.01
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
From a file:
.PP
.Vb 1
\&    bp_revtrans\-motif.pl \-i motifs.txt
.Ve
.PP
Using pipes:
.PP
.Vb 1
\&   bp_revtrans\-motif.pl < motifs.txt > output.txt
.Ve
.PP
Using interactively at the command prompt:
.PP
.Vb 5
\&   $ bp_revtrans\-motif.pl
\&   MAAEEL[VIKP]
\&   1.   ATGGCNGCNGARGARYTNVHN
\&   [^P]H(IW){2,3}
\&   2.   NDNCAY(ATHTGG){2,3}
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
The input motif consists of a string of one-letter residues, with any of
the following syntactic elements:
.IP "\fB[...]\fR : Redundant position." 4
.IX Item "[...] : Redundant position."
A position in which more than one residue is allowed. Example:
.Sp
.Vb 2
\&    [TS]YW[RKSD]
\&     ^^    ^^^^
.Ve
.IP "\fB[^...]\fR : Negated position." 4
.IX Item "[^...] : Negated position."
A position in which any residue is allowed, saved for those between
brackets. Example:
.Sp
.Vb 2
\&    [^PW]MK[LAE]
\&      ^^
.Ve
.IP "\fB(...){n,m,...}\fR : Repeated motif." 4
.IX Item "(...){n,m,...} : Repeated motif."
A motif that is repeated \fBn\fR or \fBm\fR times. It can have any of the previous
syntactic elements. Example:
.Sp
.Vb 2
\&    A[SN]C(TXX){2,4,8}
\&           ^^^
.Ve
.PP
The allowed letters are those that correspond to the 20 natural aminoacids,
plus:
.PP
.Vb 3
\&    B = N + D
\&    Z = Q + E
\&    X = All
.Ve
.SH "OPTIONS"
.IX Header "OPTIONS"
.SS "\fB\-i input-file\fP:"
.IX Subsection "-i input-file:"
A file with a list of motifs to reverse translate.
.SS "\fB\-h\fP"
.IX Subsection "-h"
Display this help message.
.SH "AUTHOR"
.IX Header "AUTHOR"
Bruno Vecchi, \f(CW\*(C`vecchi.b at gmail.com\*(C'\fR
.SH "BUGS"
.IX Header "BUGS"
Please report any bugs or feature requests to \f(CW\*(C`vecchi.b at gmail.com\*(C'\fR
.SH "COPYRIGHT & LICENSE"
.IX Header "COPYRIGHT & LICENSE"
Copyright 2009 Bruno Vecchi, all rights reserved.
.PP
This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.