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.IX Title "Bio::Tools::Run::Alignment::Sim4 3pm"
.TH Bio::Tools::Run::Alignment::Sim4 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH NAME
Bio::Tools::Run::Alignment::Sim4 \- Wrapper for Sim4 program that allows
for alignment of cdna to genomic sequences
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 1
\&  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 $exon\->start."\et".$exon\->end."\et".$exon\->strand."\en";
\&        print "\etMatched ".$exon\->est_hit\->seq_id."\et".$exon\->est_hit\->start."\et".$exon\->est_hit\->end."\en";
\&    }
\&  }
\&
\&  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 = $factory\->align(\e@est_seq,$genomic);
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Sim4 program is developed by Florea et al. for aligning cdna/est
sequence to genomic sequences
.PP
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
.PP
The program is available for download here:
http://globin.cse.psu.edu/
.SH FEEDBACK
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS Support
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Shawn Hoon"
.IX Header "AUTHOR - Shawn Hoon"
Email shawnh@fugu\-sg.org
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS program_name
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory\->program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS program_dir
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS version
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : not supported 
\& Function: Cannot determine from program 
\& Example :
\& Returns : float or undef
\& Args    : none
.Ve
.SS align
.IX Subsection "align"
.Vb 11
\& Title   : align
\& Usage   :
\&            $cdna = \*(Aqt/data/cdna.fa\*(Aq;
\&            $genomic = \*(Aqt/data/cdna.fa\*(Aq;
\&            @exon_set = $factory\->align($cdna,$genomic);
\&          or
\&            #@seq_array is array of Seq objs
\&            $cdna = \e@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.
.Ve
.SS _run
.IX Subsection "_run"
.Vb 7
\& 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
.Ve
.SS \fB_setinput()\fP
.IX Subsection "_setinput()"
.Vb 6
\& 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
.Ve
.SS \fB_setparams()\fP
.IX Subsection "_setparams()"
.Vb 7
\& 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
.Ve