| Bio::Tools::Run::Alignment::Sim4(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Alignment::Sim4(3pm) |
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");
@est_seq=();
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: http://globin.cse.psu.edu/
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.
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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.
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:
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Email shawnh@fugu-sg.org
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);
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.
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
| 2023-01-22 | perl v5.36.0 |