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

[Will McLaren]

Hi Sung

The codons() method will work; it returns the codon something like:

aGa/aCa

where the base changed is in capital letters.

Will

On 10 December 2010 11:26, Sung Gong <sung at bio.cc> wrote:
> 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
>>>
>>> _______________________________________________
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>>> Dev at ensembl.org
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>>>
>>
>