Bio::Tools::Run::Alignment::Sim4.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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
 
 

Support

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

bioperl-l@bioperl.org

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 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, obtained 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