Bio::Tools::Run::Alignment::Sim4(3pm) User Contributed Perl Documentation Bio::Tools::Run::Alignment::Sim4(3pm)
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 $exon->start." ".$exon->end." ".$exon->strand."
";
print " Matched ".$exon->est_hit->seq_id." ".$exon->est_hit->start." ".$exon->est_hit->end."
";
}
}
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://redmine.open-bio.org/projects/bioperl/
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
perl v5.12.3 2011-06-18 Bio::Tools::Run::Alignment::Sim4(3pm)