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/

Mailing Lists
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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.bioperl.org/ Email shawnh@fugu-sg.org 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