my $inputstream = Bio::SeqIO->new( -file => 'seqfile', -format => 'fasta' ); my $seqobj = $inputstream->next_seq(); my $OAF_obj = Bio::Tools::OAF->new( $seqobj );
my $array_ref = $OAF_obj->{'_result'} if ( $OAF_obj->find() );
$OAF_obj->show( 'genbank' );
#!/usr/bin/perl -w use strict; use Bio::Seq; use Bio::Tools::OAF; my $inseq = Bio::SeqIO->new( '-file' => "< $yourfile", -format => 'fasta' ); while (my $seq = $inseq->next_seq) { my $OAF_obj = Bio::Tools::OAF->new( $seq, 11 ); if ( $OAF_obj->find() ) { $OAZ_obj->show( 'genbank' ); } else { print " no hit!\n"; } }
my $nb = Bio::Tools::OAF->new( $seqobj, $table, $aug, $hmm, $fs );
my $bool = $OAF_obj->find( $evalue, $strand, $start, $end );
my @CDSData = $OAF_obj->{'_result'}; print "$CDSData[0]\n"; # detailed position of the sequence [string] print "$CDSData[1]\n"; # start position [integer] print "$CDSData[2]\n"; # stop position [integer] print "$CDSData[3]\n"; # strand (1 direct, -1 reverse) [integer] print "$CDSData[4]\n"; # Protein name [string] print "$CDSData[5]\n"; # Gene Name [string] print "$CDSData[6]\n"; # Remarques and HMMs e-values [string] print "$CDSData[7]\n"; # DNA sequence [string] print "$CDSData[8]\n"; # Protein sequence [string]The HMMs results are store in the tables $OAF_obj->{'_hmmfs'} and $OAF_obj->{'_hmmoaz'}:
my @HMMData0 = $OAF_obj->{'_hmmfs'}; # HMM details for the 5' part of the sequence print "HMMData0[0]\n"; # HMM profile name [string] print "HMMData0[1]\n"; # OAZ paralog id [integer] print "HMMData0[2]\n"; # HMM score [integer] print "HMMData0[3]\n"; # start position [integer] print "HMMData0[4]\n"; # stop position [integer] print "HMMData0[5]\n"; # strand (1 direct, -1 reverse) [integer] my @HMMData1 = $OAF_obj->{'_hmmoaz'}; # HMM details for the 3' part of the sequence print "HMMData1[0]\n"; # HMM profile name [string] print "HMMData1[1]\n"; # OAZ paralog id [integer] print "HMMData1[2]\n"; # HMM score [integer] print "HMMData1[3]\n"; # start position [integer] print "HMMData1[4]\n"; # stop position [integer] print "HMMData1[5]\n"; # strand (1 direct, -1 reverse) [integer]The sequences issues are separately store:
print '5\' of the CDS is missing: ', $OAF_obj->{'_no5'} ? 'yes' : 'no', "\n"; print '3\' of the CDS is missing: ', $OAF_obj->{'_no3'} ? 'yes' : 'no' . "\n"; print 'The position of the initiation codon is identified: ', $OAF_obj->{'_noaug'} ? 'no' : 'yes', "\n";
$OAF_obj->show( $outstyle );
my @hits = Bio::Tools::OAF->getHits( $evalue, $seq, $ref );
print join( "\n", @hits );
my $bool = Bio::Tools::OAF->ortholog( $file, $evalue, $format, $aug, $remote, $hmm, $fs, $bank, $filter, $verbose );
Michaël Bekaert School of Biology and Environmental Science University Collele Dublin Belfield Dublin 4 Ireland
Ivaylo P. Ivanov Bioscience Institute University College Cork Cork Ireland
John F. Atkins Human Genetics Department University of Utah Salt Lake City Utah USA
Pavel V. Baranov Biochemistry Department University College Cork Cork Ireland