On Mon, Aug 31, 2009 at 6:23 PM, Christopher Lee <[email protected]> wrote:
> > > On Aug 31, 2009, at 5:57 PM, Jenny Qing Qian wrote: > > > For the time being, could we include an example to show how to bind > > the ucsc gene/exon annotations to ucsc references? Has this already > > been constructed and saved for some of the ucsc reference genomes? > > If so, could you let us their names, so that we could access them > > via the worldbase? > > No, I don't think we have such annotations plugged in. Do you know if > the annotation data can be accessed from UCSC in a relatively simple > way, eg. via MySQL? In that case we could probably whip up a quick > example showing how to plug them in... 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? > > > -- 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 -~----------~----~----~----~------~----~------~--~---
