bp_revtrans-motif(1p) [debian man page]

BP_REVTRANS-MOTIF(1p)					User Contributed Perl Documentation				     BP_REVTRANS-MOTIF(1p)

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 &; 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 v5.14.2							    2012-03-02						     BP_REVTRANS-MOTIF(1p)

Bio::Matrix::PSM::PsmHeaderI(3pm)			User Contributed Perl Documentation			 Bio::Matrix::PSM::PsmHeaderI(3pm)

NAME

       Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file

SYNOPSIS

	use Bio::Matrix::PSM::IO;
	#Obtain an Bio::Matrix::PSM::IO object:
	my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'mast');

	#Get some general data about the file you are parsing:
	my $release=$psmIO->release;
	my $version=$psmIO->version;

	print "This analysis was performed using MAST version $version, release $release
";

	#Now let's see what are the consensus sequences of the motifs fed as an input:
	my %seq=$psmIO->seq;

	#let's cycle through all consensus sequences now:

	foreach my $id ($psmIO->hid) {
	  print "Motif $id is 	",$seq{$id},"
";
	}

	 #Finally look at the stuff we do not parse:
	 my @inputfile=grep(/datafile/i,$psmIO->unstructured);

DESCRIPTION

       Generally you should not use this object directly, you can access the information through a PSM driver (See Bio::Matrix::PSM::IO). It is
       handling the header data from a PSM file which may be very different. This means that some of the methods will return undef naturally,
       because this information is not present in the file which is parsed. Some important data might be left over in the unstructured part, and
       you might have to parse it yourself. I will try to 'structure' this header more in the near future.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably
	to one of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Stefan Kirov
       Email skirov@utk.edu

APPENDIX

   new
	Title	: new
	Usage	: my $header= Bio::Matrix::PSM::PsmHeader->new
		   ( -seq=>\%seq, -mid=>\%mid, -width=>\%width,
		     -instances=>\%instances, -header=>@header, -type=>'mast');
	Function: Creates a new Bio::Matrix::PSM::PsmHeader object
	Throws	:
	Example :
	Returns :  Bio::Matrix::PSM::PsmHeaderI object
	Args	:  hash

   seq
	Title	: seq
	Usage	: my %seq= $header->seq();
	Function: Returns the sequence data as a hash, indexed by a
		  sequence ID (motif id or accession number)
		  In case the input data is a motif it would return the
		  consenus seq for each of them (mast).
	Throws	:
	Example :
	Returns :  hash
	Args	:

   hid
	Title	: hid
	Usage	: my @ids= $header->hid();
	Function: Returns array with the motif/instance ids
	Throws	:
	Example :
	Returns :  array
	Args	:

   length
	Title	: length
	Usage	: my %length= $header->length();
	Function: Returns the length of the input sequence or motifs as a hash, indexed
		  by a sequence ID (motif id or accession number)
	Throws	:
	Example :
	Returns :  hash
	Args	:

   instances
	Title	: instances
	Usage	: my %instances= $header->length();
	Function: Returns the instance, used  as a hash, indexed
		  by a sequence ID (motif id or accession number)
	Throws	:
	Example :
	Returns :  hash of Bio::Matrix::PSM::InstanceSite objects
	Args	:

   weights
	Title	: weights
	Usage	: my %weights= $header->weights();
	Function: Returns the weights of the input sequence as a hash, indexed
		  by a sequence ID
	Throws	:
	Example :
	Returns :  hash
	Args	:

   unstuctured
	Title	: unstuctured
	Usage	: my @unstructured= $header->unstuctured();
	Function: Returns the unstructured data in the header as an array, one line per
		  array element, all control symbols are removed with W
	Throws	:
	Example :
	Returns :   array
	Args	:

   version
	Title	: version
	Usage	: my $version= $header->version;
	Function: Returns the version of the file being parsed if such exists
	Throws	:
	Example :
	Returns :  string
	Args	:

   revision
	Title	: revision
	Usage	: my $revision= $header->revision;
	Function: Returns the revision of the file being parsed if such exists
	Throws	:
	Example :
	Returns :  string
	Args	:

   _check
	Title	: _check
	Usage	: if ($self->_check('weights') { #do something} else {return 0;}
	Function: Checks if the method called is aplicable to the file format
	Throws	:
	Example :
	Returns :  boolean
	Args	:  string

perl v5.14.2							    2012-03-02					 Bio::Matrix::PSM::PsmHeaderI(3pm)