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Bio::Tools::Run::AlignUser:Contributed PerlBio::Tools::Run::Alignment::Sim4(3)

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

	 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 $exon->start."\t".$exon->end."\t".$exon->strand."\n";
	       print "\tMatched	".$exon->est_hit->seq_id."\t".$exon->est_hit->start."\t".$exon->est_hit->end."\n";

	 One can also provide a	est database

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

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

       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:

   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.			- General discussion	- About	the mailing lists

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

       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

AUTHOR - Shawn Hoon

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

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

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

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

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

	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

	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

	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 v5.32.1			  2021-03-0Bio::Tools::Run::Alignment::Sim4(3)


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