[ensembl-dev] Homopolymeric regions and snp

[Will McLaren]

Hi Matteo,

We don't have a specific tool or functionality for discovering
homopolymeric regions.

If I were to approach this problem I'd write a short script to look up some
amount of reference sequence either side of the SNP position and check it
for homopolymerism.

In Perl you could use the Ensembl API [1] or use the BioPerl Bio::DB::Fasta
[2] module and a FASTA file of the genome.

You may also consider using our REST API to retrieve the sequence, which
can be scripted against using any language [3].

Hope that helps

Will McLaren
Ensembl Variation

1: http://www.ensembl.org/info/docs/index.html
2: http://search.cpan.org/dist/BioPerl/Bio/DB/Fasta.pm
3: http://rest.ensembl.org/documentation/info/sequence_region

On 10 May 2016 at 11:31, Matteo <matteodeg at gmail.com> wrote:

> Hi all,
>
> I have a question for you. I'm using Grch37 and I'm looking for a solution
> about homopolymeric regions. I'd like to get an additional annotation if a
> snp or Indel is in an homopolymeric region. Do you have any idea about
> this? Is there any Ensembl solution to get this annotation on a vcf format?
>
> Thank you very much,
>
> Matteo
>
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