[ensembl-dev] RefSeq <-> Ensembl Transcript ID?

[Cei Abreu-Goodger]

Ah, now that sounds exactly like what I need. They do appear to be 
stored at the protein level, so, I can find the RefSeq transcript 
mappings by using get_all_DBLinks instead of DBEntries:

    my $dblinks = $tr -> get_all_DBLinks();
    while (my $dblink = shift @$dblinks) {
	my $db_name = $dblink -> dbname() || "";
	next unless ($db_name eq "RefSeq_dna" or $db_name eq 
"RefSeq_dna_predicted");
	...
    }

This sounds like there is no mapping for non-coding transcripts, is this 
correct?

Thanks,

Cei


On 07/10/2010 15:15, Ewan Birney wrote:
>
> It is done at the transcript level (not the gene level) though I can't
> remember (and it might have changed) whether the Xref stores it
> at the protein or cDNA level.
>
> In Ensembl there is a 1 to 1 link between proteins and transcripts,
> so mapping "at the protein level" (in terms of how it is stored)
> is the same as the cDNA level.
>
> I am pretty sure we now do quite alot of the Xref mapping at the
> cDNA level to help resolve very close paralogs - Ian and Glenn to
> confirm.
>
>
> On 7 Oct 2010, at 15:01, Cei Abreu-Goodger wrote:
>
>> Thanks Bert and Sergei,
>>
>> Yeah, I was kind of hoping that there would be a direct relationship
>> between transcripts. But if the connection is done at the protein
>> level, I'll have to drop down to gene IDs.
>>
>> Does anyone in Ensembl know if there's a plan to perform mapping at
>> the transcript level to UCSC or NCBI?
>>
>> Cheers,
>>
>> Cei
>>
>> On 07/10/2010 14:57, Bert Overduin wrote:
>>> Hello Cei,
>>>
>>> I think the NCBI RefSeq IDs are on the level of the translation, not the
>>> transcript. So, you have to get the DBEntries for the translation of
>>> your
>>> transcript or alternatively get the DBLinks for your transcript.
>>>
>>> Cheers,
>>> Bert
>>>
>>> On Thu, Oct 7, 2010 at 2:40 PM, Cei Abreu-Goodger<cei at ebi.ac.uk> wrote:
>>>
>>>> Hello,
>>>>
>>>> Is it possible to obtain the relationship between Ensembl Transcript
>>>> IDs
>>>> and NCBI's RefSeq transcript ids (NM_########)? I've been searching
>>>> in the
>>>> DBEntries assigned to the transcripts, but can't seem to find this.
>>>>
>>>> Thanks!
>>>>
>>>> Cei
>>>>
>>>> _______________________________________________
>>>> Dev mailing list
>>>> Dev at ensembl.org
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev