Thanks Jennifer, but I'm querying the colors remotely by retrieving the database tables and not through an internet browser. I was able to determine gene colors with the information in the kgColor table for "hg19", "hg18". But earlier assemblies don't have the kgColor table. Is there a different table for the earlier assemblies where gene colors are specified?
Thanks, Sigal On Mon, May 03, 2010 at 02:45:04PM -0700, Jennifer Jackson wrote: > Hello Sigal, > > Color coding is defined in the Known Genes track description page, > in the second section under "Methods". See the actual html page for > the links out to additional information. > > Display Conventions and Configuration > > This track follows the display conventions for gene prediction > tracks with the following color scheme: > > Black: indicates the gene has a corresponding entry in the Protein > Databank (PDB). > Dark Blue: indicates the gene has either a corresponding RefSeq mRNA > that is "Reviewed" or "Validated" or a corresponding Swiss-Prot > protein. > Medium Blue: indicates the gene has a corresponding RefSeq mRNA that > is not "Reviewed" nor "Validated". > Light Blue: everything else. That is, the gene does not have a > corresponding Protein Databank entry, RefSeq mRNA, or Swiss-Prot > protein, but it has supporting evidence of a GenBank mRNA with a > UniProt (TrEMBL) protein. > > This track contains an optional codon coloring feature that allows > users to quickly validate and compare gene predictions. To display > codon colors, select the genomic codons option from the Color track > by codons pull-down menu. Click here for more information about this > feature. > > Thanks, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/3/10 2:29 PM, Sigal Blay wrote: > >The color coding is contained in the UCSC Gene track associated > >table "kgColor" for hg19 and hg18. > >what about earlier assemblies? > > > >Thanks! > >Sigal _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
