Provided by: libbio-perl-run-perl_1.7.3-3_all bug


       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

       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