[Bioperl-l] Overlapping Features with GFF dbase

Victor victor.ruotti at gmail.com
Thu Jul 7 11:05:24 EDT 2005

I was wondering if someone can point me out on how best to retrieve a set of 
overlapping features from the GFF schema. Right now I am looking at the 
GFF.pm <http://GFF.pm> to do this by:

use Bio::DB::GFF;
my $db = Bio::DB:GFF->new(-dsn =>'mydbase',
-aggregators =>'gene_model{CDS ,five_prime_UTR,three_prime_UTR'});

my $gene_stream = $db=>get_seq_stream('gene_model:UCSC_hg16');

while (my $gene = $gene_stream->next_seq) {
print $gene->name, "\n";
for my $part ($gene->get_SeqFeatures) {
print "\t", join("\t", $part->method,$part->start,$part->end), "\n";
print "\n";

This gets all the genes from the GFF schema. Should I be using another while 
loop to retrieve other features that overlap with these genes? It there a 
bioperl module to retrieve overlapping features? I would like to be able to 
get all the features that overlap with a particular gene or a whole set of 

Thanks in advance.

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