Bio::Tools::Run::Alignment::Sim4(3pm)			User Contributed Perl Documentation		     Bio::Tools::Run::Alignment::Sim4(3pm)

NAME

       Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences

SYNOPSIS

	 use Bio::Tools::Run::Alignment::Sim4;

	 my @params = (W=>15,K=>17,D=>10,N=>10,cdna_seq=>"mouse_cdna.fa",genomic_seq=>"mouse_genomic.fa");
	 my $sim4 = Bio::Tools::Run::Alignment::Sim4->new(@params);

	 my @exon_sets = $sim4->align;

	 foreach my $set(@exon_sets){
	   foreach my $exon($set->sub_SeqFeature){
	       print $exon->start."	".$exon->end."	".$exon->strand."
";
	       print "	Matched ".$exon->est_hit->seq_id."	".$exon->est_hit->start."	".$exon->est_hit->end."
";
	   }
	 }

	 One can also provide a est database

	$sio = Bio::SeqIO->new(-file=>"est.fa",-format=>"fasta");
	@est_seq=();
	while(my $seq = $sio->next_seq){
		push @est_seq,$seq;
	}

	my @exon_sets = $factory->align(@est_seq,$genomic);

DESCRIPTION

       Sim4 program is developed by Florea et al. for aligning cdna/est sequence to genomic sequences

       Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W.  A computer program for aligning a cDNA sequence with a genomic DNA sequence.  Genome
       Res 1998 Sep;8(9):967-74

       The program is available for download here: http://globin.cse.psu.edu/

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:

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

AUTHOR - Shawn Hoon
       Email shawnh@fugu-sg.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   program_name
	Title	: program_name
	Usage	: $factory->program_name()
	Function: holds the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns:  string
	Args	:

   version
	Title	: version
	Usage	: not supported
	Function: Cannot determine from program
	Example :
	Returns : float or undef
	Args	: none

   align
	Title	: align
	Usage	:
		   $cdna = 't/data/cdna.fa';
		   $genomic = 't/data/cdna.fa';
		   @exon_set = $factory->align($cdna,$genomic);
		 or
		   #@seq_array is array of Seq objs
		   $cdna = @seq_array;
		   @exon_set = $factory->align($cdna,$genomic);
		 of
		   @exon_set = $factory->align($cdna->[0],$genomic)

	Function: Perform a Sim4  alignment
	Returns : An array of Bio::SeqFeature::Generic objects which has
		  exons as sub seqfeatures.
	Args	: Name of two files containing fasta sequences,
		  or 2 Bio::SeqI objects
		  or a combination of both
		  first is assumed to be cdna
		  second is assumed to be genomic
		  More than one cdna may be provided. If an object,
		  assume that its an array ref.

   _run
	Title	:  _run
	Usage	:  Internal function, not to be called directly
	Function:   makes actual system call to Sim4 program
	Example :
	Returns : nothing; Sim4  output is written to a temp file
	Args	: Name of a file containing a set of unaligned fasta sequences
		  and hash of parameters to be passed to Sim4

   _setinput()
	Title	:  _setinput
	Usage	:  Internal function, not to be called directly
	Function:   Create input file for Sim4 program
	Example :
	Returns : name of file containing Sim4 data input
	Args	: Seq or Align object reference or input file name

   _setparams()
	Title	:  _setparams
	Usage	:  Internal function, not to be called directly
	Function:   Create parameter inputs for Sim4 program
	Example :
	Returns : parameter string to be passed to Sim4
		  during align or profile_align
	Args	: name of calling object

perl v5.12.3							    2011-06-18				     Bio::Tools::Run::Alignment::Sim4(3pm)