Well, actually none! We work with plant genomes sequenced and annotated here (at JGI) as well as pulled from a variety of external sources (TIGR/MSU, Genoscope, Maizesequence.org, etc.), and their stored in our plant comparative database (not based on any of the standard open source schemas out there).
My motivation in getting pygr fetching from GBrowse and/or BioMart is that we already push from our db to these two systems, and want to develop UCSC table browser style capabilities without the UCSC back and frontends. Since pygr provides overlap calculation (the heart of the table browser capability) perfomance comparable to (and even faster) than what UCSC enables via binning, we though if we "shadowed" our BioMart or GBrowse systems with some of pygr's database objects, we'd have the best of both worlds. So that's why we're looking at pygr fetch from Gbrowse/GFF or BioMart. --David On 3 Jun 2009, at 10:26, Jenny Qing Qian wrote: > Hi David, > > What sorts of ensembl datasets are you mostly interested in? Which > database would you like to interface with first? > > Cheers, > Jenny > > On Tue, Jun 2, 2009 at 8:49 PM, David Goodstein > <dmgoodst...@lbl.gov> wrote: > Thanks Jenny. It will be worthwhile taking a look at the steps you > followed to interface with Ensembl. > > --David > David M. Goodstein > Computational Genomics and Plant Genomics Program > Joint Genome Institute > USDOE - Lawrence Berkeley National Lab > http://www.phytozome.net > > On Jun 2, 2009, at 6:58 PM, Jenny Qing Qian wrote: > >> Hi Titus and David, >> >> My ENSEMBL interface relies on Pygr code added after the latest >> public Pygr release pygr-0.7.1.tar.gz. To get a working copy, you >> could pull from git://github.com/jqian/pyensembl.git. This >> interface is handy in importing Ensembl annotation datasets into >> Pygr worldbase. >> >> Cheers, >> Jenny >> >> On Tue, Jun 2, 2009 at 6:05 PM, C. Titus Brown <c...@msu.edu> wrote: >> >> On Tue, Jun 02, 2009 at 05:23:36PM -0700, dmgood11 wrote: >> -> I was wondering if there had been any work on supporting >> fetches from >> -> BioMart or GBrowse/GFF databases (for those of us whose genomic >> data >> -> are not stored in Santa Cruz format)? >> >> Hi David, >> >> none that I know of, although Jenny Qian worked on an ENSEMBL >> interface >> -- you can take a look at it here, >> >> http://pygr.googlecode.com/files/pyensembl-0.1.0.tar.gz >> >> although I think it is not yet mature. Jenny, any comments? >> >> I expect to write some wrappers to load in GFF3 later this >> summer. I'll >> post them here as I work on it. >> >> cheers, >> --titus >> -- >> C. Titus Brown, c...@msu.edu >> >> >> >> >> > > > > > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
