[ensembl-dev] CDS Incomplete status

[mag]

Hi Konrad,

The transcript object supports a method called 'transleatable_seq'.
This will return the translateable part of a transcript.
You can then apply the length method on the returned string.

The CDS incomplete status is only available for manually annotated genes 
(coming from Havana).
They know there is a protein-coding transcript, but the evidence 
available does not allow for full annotation of the sequence.
These transcripts are flagged with the attribute 'cds_start_NF' or 
'cds_end_NF'
You can retrieve this for each transcript using 
$transcript->get_all_Attributes('cds_start_NF')
or retrieve all the transcripts for a given attribute using 
$attribute_adaptor->fetch_all_by_Transcript(undef, 'cds_start_NF')


Hope that helps,
Magali

On 24/04/2014 21:47, Konrad Karczewski wrote:
> Hello!
>
> I've been using the API to get the length of the coding portion of a 
> transcript and I think I figured out the best way is:
>
> my $transcript_cds_length = 
> $transcript_variation->transcript->cdna_coding_end - 
> $transcript_variation->transcript->cdna_coding_start + 1;
>
> However, for some transcripts, this number is not a multiple of 3 
> (though it is approximately correct - within 2 bp of the number of 
> AA's of the transcript * 3). It seems to happen when there is a "CDS 
> Incomplete" status on the transcript (e.g. 
> http://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000162458;r=1:16084441-16091522;t=ENST00000510929). 
> I would have thought if the CDS were incomplete then "cdna_coding_end" 
> or "cdna_coding_start" would be undefined - is there another way to 
> get the CDS Incomplete status?
>
> And side note, is this the best way to get transcript length? I 
> couldn't seem to find a direct reference to the length.
>
> Thanks!
> -Konrad
>
>
>
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