pureGFF indexer

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pureGFF indexer

Postby baj09 » Thu Jun 18, 2009 9:53 am

Hi,

I am trying to set up a flybase GenomeBrowse (1.69) instance in our institute. I.e. I want to use GBrowse with the pureGFF adapter. I was given a link to the source but apparently i need to index the GFF files. And I don't know how to do this. Could anyone please help?

Thanks,

Bernd
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Re: pureGFF indexer

Postby strelets » Thu Jul 16, 2009 12:50 pm

Sorry for the delay with answer..

In the same directory (and accessable from page of description
of these adaptor-related things) is a gzipped tar of all related
software, which should include indexer script too. Just to
simplify download for you I just installed that script as an
independent entity in there and you can retrieve it using URL

flybase.org/static_pages/docs/software/index_gff_files.pl.gz

Regards,

V. Strelets
FlyBase Consortium
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Re: pureGFF indexer

Postby malcook » Thu Jul 16, 2009 1:32 pm

Hi,

Can you also provide links to information/source for "the pureGFF adapter". I can't find it mentioned elsewhere.

Thanks,

Malcolm Cook
Malcolm Cook - Stowers Institute for Medical Research
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Re: pureGFF indexer

Postby strelets » Fri Jul 17, 2009 10:52 am

Short description of this adaptor can be viewed at

flybase.org/static_pages/docs/software

There was no intent to actually advertise it to other
projects or to make it conveniently accessible to
potential users. It powers FlyBase GBrowse and
was written with just one goal in mind - to have
an adaptor which shows good performance (and low
maintenance) when other adaptors choke (like we
have 16 viewable genomes, any one can have
like 20 million features [Dmel] or like 10 thousand
separate sequenced contigs [Dana Dper and others]).
It is kind of internal thingie, to serve project needs..

V. Strelets
FlyBase Consortium
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