[ensembl-dev] repeatmasker version information of the masked genome sequences

[Andy Yates]

Hi Pengcheng,

We do not provide the repeats in any flat file format. My best suggestion would be to use the Perl API to extract the repeats you require. The Ensembl tutorial provides information about how to get a hold of the repeat features:

http://www.ensembl.org/info/docs/api/core/core_tutorial.html

Hope this helps,

Andy

On 16 Dec 2010, at 01:47, Pengcheng Yang wrote:

> Hi Andy,
> 
> Thanks for your reply.
> Is there a summary file, in GFF format, of the repeats in the genome sequences?  From the summary GFF files, we can get the statistics that how many are every kind of repeats.
> 
> Regards,
> Pengcheng
> 
> 
> On 2010-12-15 0:22, Andy Yates wrote:
>> Dear Pengcheng,
>> 
>> Much like UCSC we in EnsemblGenomes use the latest version of RepeatMasker (open-3.2.9).
>> 
>> Regards,
>> 
>> Andy
>> 
>> On 14 Dec 2010, at 16:16, Pengcheng Yang wrote:
>> 
>>> Hi,
>>> 
>>> I can not find the RepeatMasker Version information in the ensemblgenomes.org,  as UCSC Genome Browser supplied http://genome.ucsc.edu/FAQ/FAQdownloads.html#download16.
>>> 
>>> Thanks,
>>> 
>>> Pengcheng
>>> 
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/