[ensembl-dev] db_version in function ' fetch_by_region '

mamunur.rashid rm8 at sanger.ac.uk
Tue May 8 12:38:17 BST 2012


Hi All,
I am trying to extract sequence information from ensembl using 2 different human genome build.

I have a two different sets of genomic locations, first one from hg19 build and second from hg18 build.



I use the following code bit
# ------------------- #
     $registry->load_registry_from_db( -host =>  'ensembldb.ensembl.org', -user=>  'anonymous' );
     my $human_slice_adaptor = $registry->get_adaptor( $species,'Core','Slice');
     my $slice = $human_slice_adaptor->fetch_by_region('chromosome', $chr_name , $start , $end , $dbversion );
     my $sequence = $slice->seq();
# ------------------- #

Does anyone can give me some idea about the possible values of the " $dbversion " parameter for hg19 and hg18 build.

I have tried using GRCh37 -and  NCBI36 respectively but it returns me values from current genome build anyway.


thanks in advance,
Mamun





More information about the Dev mailing list