[ensembl-dev] Prediction of consequence type for novel variants

Sung Gong sung at bio.cc
Fri Dec 10 11:26:04 GMT 2010


Hi Will,

Thanks for the paper. I appreciate your work.

Before aware of your script, I used to get the corresponding codon and
the position (0, 1 or 2) where a single DNA variant occur using the
core API.
Any work-around for this?

I found a 'codons' method from 'TranscriptVariation', but it is a
method of ConsequenceType?

Thought better to ask you before going further.

Cheers,
Sung

On 9 December 2010 14:02, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Hi Sung,
>
> There is a publication referring to the system, but it does not go
> into great detail on the internal workings:
>
> http://bioinformatics.oxfordjournals.org/content/26/16/2069.abstract
>
> Here's an approximate flow of what happens in the API. The vast
> majority of the code used is in the Core module
> Bio::EnsEMBL::Utils::TranscriptAlleles.pm, mainly the methods
> type_variation() and apply_aa_change():
>
> - find overlapping transcripts (using $vf->feature_Slice and
> $slice->get_all_Transcripts), then for each transcript:
>
> - get transcript mapper and map variation's coordinates to cDNA, CDS and peptide
>
> - any variants that don't fall in the coding sequence are classified
> here (e.g. INTRONIC, UPSTREAM) and the flow ends
>
> - if variation falls in exon (i.e. has defined CDS coordinates),
> generate alternative codon(s) and resulting translation
>
> - compare translation to reference; classify as e.g.
> SYNONYMOUS_CODING, NON_SYNONYMOUS_CODING
>
> We are currently working on an overhaul to this system which should
> make it easier to comprehend by following the code.
>
> I would recommend trying to follow through the code in Perl's
> debugger, using the "perl -d" option.
>
> Hope this helps
>
> Will McLaren
> Ensembl Variation
>
> On 9 December 2010 13:19, Sung Gong <sung at bio.cc> wrote:
>> Hi,
>>
>> I was thrilled to find that Ensembl API provides a nice script
>> (ftp://ftp.ensembl.org/pub/misc-scripts/) which can predict the
>> consequence types of novel variations.
>> Also, good to see a good demonstration how to use the API for that purpose:
>> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html
>>
>> Before realising the variation API can help predicting consequence
>> type of novel variants, I used to use only core API to map the
>> position of my variants to see whether they are within coding region,
>> intron, exon and so on.
>> Now, I wondered how the variation API works for that purpose - looked
>> at the source code, but found it is somewhat overwhelming.
>>
>> Can anybody explain how the novel prediction works internally under the hood?
>>
>> Cheers,
>> Sung
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>>
>




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