[ensembl-dev] Getting variation consequence predictions without perl

[Fiona Cunningham]

if you do not want to use Perl, there is an online version of the SNPs
effect predictor here:
http://www.ensembl.org/Homo_sapiens/UserData/UploadVariations

Fiona

------------------------------------------------------
Fiona Cunningham
Ensembl Variation Project Leader
www.ensembl.org
www.lrg-sequence.org
European Bioinformatics Institute
t: 01223 494612 || e: fiona at ebi.ac.uk



On 14 September 2010 13:14, Asraniel <asraniel at fryx.ch> wrote:
> I got that part.
> But this only tells me the variants that are already known.
>
> I want to know the consequence of a random variant at a random position not
> yet know.
> The perl api can tell me what the consequence is for a specific transcript.
> Biomart does not seem to allow me to do that...
>
> Beat Wolf
>
> Am Dienstag 14 September 2010, um 13.58:55 schrieben Sie:
>>   Yes, Ensembl Variation -> Homo Sapiens Variation will get you human
>> variation data. To get the transcript consequences, you'll find them
>> under Attributes -> Gene associated information -> Consequence to
>> transcript.
>>
>> There is also the option to filter results by consequence, you'll find
>> that under Filters -> Gene associated variation filters -> Consequence
>> type.
>>
>> Hope this helps!
>> /Pontus
>>
>> On 14/09/2010 12:04, Asraniel wrote:
>> > Sounds great.
>> >
>> > I'm no biologist, so i'm not sure what biomart to choose.
>> >
>> > For the known variations i use:
>> > Ensembl Variation 59
>> > Homo sapiens Variation (dbSNP 131; ENSEMBL).
>> >
>> > what would i have to choose for the predicted variants?
>> >
>> > thank you
>> >
>> > Beat Wolf
>> >
>> > Am Dienstag 14 September 2010, um 12.58:39 schrieben Sie:
>> >>    Hi,
>> >>
>> >> There is a dedicated BioMart for Ensembl Variation data which contains
>> >> the predicted transcript consequences
>> >> (http://www.ensembl.org/biomart/martview). Could you extract them from
>> >> there?
>> >>
>> >> Cheers
>> >> /Pontus
>> >>
>> >> On 14/09/2010 11:42, Asraniel wrote:
>> >>> Thanks for your answer.
>> >>>
>> >>> Sadly this is not an option, because my app has to work on
>> >>> linux/windows/mac and is started trough webstart, so i can't expect
>> >>> that everybody has a perl interpreter installed.
>> >>>
>> >>> Beat Wolf
>> >>>
>> >>> Am Dienstag 14 September 2010, um 12.39:54 schrieb Stuart Meacham:
>> >>>> Hi there,
>> >>>>
>> >>>> This is probably not going to answer your question! However I also
>> >>>> developed a Java app and wanted to use the SNP consequence prediction
>> >>>> script (or variations thereof). My first attempt was to just execute
>> >>>> the script from within the app with a call to:
>> >>>>
>> >>>> ///////////////
>> >>>>
>> >>>> Process p = Runtime.getRuntime().exec("/path/to/script/script.pl");
>> >>>>
>> >>>> //////////////
>> >>>>
>> >>>> and then reading the output of the script with:
>> >>>>
>> >>>> //////////////
>> >>>>
>> >>>> BufferedReader stdInput = new BufferedReader(new
>> >>>> InputStreamReader(p.getInputStream()));
>> >>>>
>> >>>> String s = null;
>> >>>>
>> >>>> while ((s = stdInput.readLine()) != null) {
>> >>>>
>> >>>>  //do stuff with s
>> >>>>
>> >>>> }
>> >>>>
>> >>>> //////////////
>> >>>>
>> >>>> This works fine although can be slow, and the speed is erratic,
>> >>>> especially if your app is going to support many concurrent users. In
>> >>>> order to traverse this problem I implemented a second version which
>> >>>> simply ran the script independently (outside the app) saved the output
>> >>>> to a database and read the database from the app.
>> >>>>
>> >>>> I do remember having a conversation once with an Ensembl Dev who said
>> >>>> that there was a Java API a few years ago but it now lacks support and
>> >>>> is obviously out of date.
>> >>>>
>> >>>> Good luck!
>> >>>>
>> >>>> Stuart
>> >>>>
>> >>>> On 14/09/10 11:22, Asraniel wrote:
>> >>>>> Hi,
>> >>>>>
>> >>>>> i'm developing java app and i access the ensembl data trough biomart.
>> >>>>> Works great, thanks for that api.
>> >>>>>
>> >>>>> Now, is there a way to get the variantion consequence prediction
>> >>>>> without using perl? i didn't find a way trough biomart.
>> >>>>>
>> >>>>> Thank you
>> >>>>>
>> >>>>> Beat Wolf
>> >>>>>
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