[ensembl-dev] Missing IDS in ENSEMBL database
Duarte Molha
Duarte.Molha at ogt.co.uk
Fri May 25 12:02:11 BST 2012
Thanks Thibaut Hourlier
I just get very confused with all these IDS with the same format meaning different things!
Best regards
Duarte
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Thibaut Hourlier
Sent: 25 May 2012 11:20
To: Ensembl developers list
Subject: Re: [ensembl-dev] Missing IDS in ENSEMBL database
Dear Duarte,
I went through the four first of your IDs:
On 25 May 2012, at 10:14, Duarte Molha wrote:
Dear Developers
I created a simple script to output the exons of specific transcripts with NM ids.
It works fine for all but a small list of IDS. The large majority of the failed IDS have been suppressed from NCBI
Because they were found to be a " nonsense-mediated mRNA decay (NMD) candidate" so I do not mind eliminating those records from my query.
However some of the ones that fail are in NCBI database and for some reason ENSEMBL is not able to query them:
NM_001040409.1
It is an NMD transcript.
NM_001167607.1
It is an exon supporting feature and not a transcript supporting feature, i think this is the reason you don't get it with your script
http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000196743;r=5:150591711-150650001;t=ENST00000523466
NM_001199987.1
If you look in the Gene database at NCBI you will see that there is 2 other sequences for NDUFB6, which are the transcript supporting feature for the 2 transcripts in Ensembl for the gene.
http://www.ncbi.nlm.nih.gov/gene/?term=NM_001199987.1
http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000165264;r=9:32552997-32573160;t=ENST00000379847
NM_001204090.1
Same problem as above, we did not use this sequence.
What you can do is to use the HGNC identifier of these failing IDs in the fetch_all_by_external_id method, i.e. NM_001199987.1 -> NDUFB6
Regards
Thibaut
NM_001242881.1
NM_014249.2
NM_015584.3
NM_024728.2
Can you tell me how to retrieve these from the database?
Here is the portion of my script I use to retrieve the data:
foreach my $query_transcript (@transcripts_of_interest) {
chomp $query_transcript;
my $transcript = "";
if ($query_transcript =~ /ENST/i){
$transcript = $transcript_adaptor->fetch_by_stable_id("$query_transcript");
}
else{
($transcript) = @{ $transcript_adaptor->fetch_all_by_external_name("$query_transcript");
}
unless ($transcript){
$progress->message("Query: $query_transcript failed");
next;
}
foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
my $estring = feature2string($exon);
print "$query_transcript:\t$estring\n";
}
$next_update = $progress->update() if (++$j > $next_update);
}
Best regards
Duarte Molha
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