[Bioperl-l] SeqIO tag/location question

Tom Keller kellert at ohsu.edu
Tue Jul 6 17:54:36 EDT 2010


Greetings,
A genbank file I am working with has features:
 exon            37167..37302
                     /gene="SLC12A3"
                     /gene_synonym="FLJ96318; NCCT; TSC"
                     /inference="alignment:Splign:1.39.8"
                     /number=24
     exon            39189..39256
                     /gene="SLC12A3"
                     /gene_synonym="FLJ96318; NCCT; TSC"
                     /inference="alignment:Splign:1.39.8"
                     /number=25
     exon            48058..50644
                     /gene="SLC12A3"
                     /gene_synonym="FLJ96318; NCCT; TSC"
                     /inference="alignment:Splign:1.39.8"
                     /number=26

When I parse it using:
my $db = Bio::DB::RefSeq->new();
my $seq = $db->get_Seq_by_acc($accession);
my @features = $seq->get_SeqFeatures;
for my$feat_obj ( @features ) {
if ($feat_obj->primary_tag eq 'exon') {
print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n";
for my $tag ($feat_obj->get_all_tags) {
for my $value ($feat_obj->get_tag_values($tag)) {
print "    value: ", $value, "\n";
}
}
}
}

I get the following:
primary tag: exon start: 42167 end: 42302
    value: SLC12A3
    value: FLJ96318; NCCT; TSC
    value: alignment:Splign:1.39.8
    value: 24
primary tag: exon start: 44189 end: 44256
    value: SLC12A3
    value: FLJ96318; NCCT; TSC
    value: alignment:Splign:1.39.8
    value: 25
primary tag: exon start: 53058 end: 55644
    value: SLC12A3
    value: FLJ96318; NCCT; TSC
    value: alignment:Splign:1.39.8
    value: 26

Where does the discrepancy in location (+5000) come from?

thanks for your help,
Tom
MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
4-2442
kellert at ohsu.edu<mailto:kellert at ohsu.edu>
RJH (CROET/BasicScience) 6339b








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