/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Alignment::Sim4

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 $exon->start."\t".$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");
@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

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://bugzilla.open-bio.org/

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, obtiained 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