On Mon, Aug 31, 2009 at 6:50 PM, Namshin Kim <[email protected]> wrote:
> > > On Tue, Sep 1, 2009 at 10:45 AM, Jenny Qing Qian <[email protected]>wrote: > >> >> >> 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? >> > > 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. 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 -~----------~----~----~----~------~----~------~--~---
