Hi,
I’d like to be able to map a list of ENSEMBL ids to WormBase sequence ids.
I see on the page:
http://www.wormbase.org/db/misc/etree?name=CN797654;class=Sequence
That there is a mapping between :
CN797654
and the matching_CDS: Y79H2A.1a
Is there a query that could do this conversion for a list of ENSEMBL ids?
Thanks,
Lisa
That is an EST from EMBL/DDB/GenBank which aligns to the C.elegans Y79H2A.1a CDS and Y79H2A.1a.1 Transcript.
It does not imply that the sequence of Y79H2A.1a.1 and CN797654 is the same.
For EnsEMBL you also don’t need a WormBase to EnsEMBL id mapping, as I used the WormBase Sequence Names as EnsEMBL GeneIds.
It should be also possible to use WQL to get the matching_CDS for a list of sequence ids (like EMBL accessions) … but I have to look that up in the WormBase Wiki, to get a nicely formatted result set.
Michael
Hi Lisa -
This script will do the mapping for you against the WormBase open access data mining server.
Usage:
ensembl2cds.pl accession_ids.txt
–
#!/usr/bin/perl
use strict;
use Ace;
my $ace = Ace->connect(-host => ‘aceserver.cshl.org’,
-port => ‘2005’) or die “Sorry, I was unable to connect to the remote WormBase database…\n”;
my $version = $ace->status->{database}{version};
open OUT,">$version-ensembl2CDS.txt";
while (<>) {
chomp;
my $sequence = $ace->fetch(Sequence => $_);
my $cds = $sequence->Matching_CDS;
my $gene = $cds->Gene if $cds;
print OUT join("\t",$sequence,$cds,$gene),"\n";
}