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. -- 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 -~----------~----~----~----~------~----~------~--~---
