On Tue, Sep 1, 2009 at 12:01 AM, Christopher Lee <[email protected]> wrote:
> > > On Aug 31, 2009, at 7:03 PM, Jenny Qing Qian wrote: > > > As the ensembl database, the ucsc database has various kinds of > > annotation feature tables like exons and genes. I am not sure > > whether they also have a seq_region table. I assume they directly > > map their annotations to their reference genomes, not via > > contigs... If this is the case, then we could just simplify the > > seqregion.py and work out the mapping. Agree? > > > > There is no seqregion table. > > > > Thanks. That helps to simplify the case. If they don't store the > > sequences at contig-level in a separate table, they probably don't > > need a seqregion table for coordinates transformation. > > I'd expect that UCSC would map the Ensembl annotations directly onto > their own assembly (i.e. no more seq_region; "stop the madness!"), and > it sounds like that's what they've actually done. If you can identify > a few candidate tables in their MySQL server that store gene and exon > annotations, we can quickly do an experiment to see how hard it would > be to plug these annotations into Pygr. I bet it'll be > straightforward, and could be good to include in the tutorial. Sounds good. We could try gene and exon tables as a start... Namshin, is there a known alternative splicing table as well? thanks, Jenny > > > -- Chris > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
