Hello, The basic query path would be to: 1) identify regions with your motif and save/load as a custom track 2) create a custom track of the upstream genomic from your transcription start sites (BED format) 3) using table browser, use the custom track from #2 and intersect against #1
A similar question was recently answered that will help to create #1: https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019300.html Here is a FAQ for #2: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks The Table browser user's guide provides step-by-step instructions for #3: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SimpleIntersection Some clarifications of the Browser's coordinate system (very important to know about when data is stranded, as your will be): http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Anton Kratz wrote: > Dear Genome Browser team, > > Is there a track that has start-end positions of TATA-Boxes on hg18? > > I have a list of a few thousand gene transcription start sites and want to > check how many of them have a TATA-Box motif in the upstream proximity > (50bp's or something like that). > > Anton > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
