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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:


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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