Hello Max, The output from the get DNA feature is extracting all data from the TFBS Conserved track, not only those features that pass the filtering criteria set on the TFBS Conserved track's description/control page.
To view this filter, go back into the browser and open the region. Next, click on the TFBS Conserved track name. Note the track control a the top that include the Z score filer. Z score cutoff (default 2.33, minimum 1.64): <replace with 1.64 here> Now, change this to be 1.64 instead of the default 2.33 or whatever else you may have set it to. Submit and you will be able to view all of the regions displayed in the browser. It is possible to just extract regions of genomic that correspond to TFBS Conserved areas at whatever threshold you desire (use the Table browser, the filter feature, and sequence output). Maybe this will work for your purposes? I will forward this off to the development team for review. It may not be possible to have the get DNA tool inherit filter options set in the browser, but it seems worth asking about, as it does create some confusion between the expected and the actual result returned. Thank you for sharing your example in such a clear way, it is very much appreciated. If you need any Table browser help, please let us know. Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/5/10 11:57 AM, Seibold, Max wrote: > Hi, > > > I am searching the sequence chr11:1197400-1200872 in Hg18 for conserved TF > binding sites using the "TFBS Conserved" track. On the browser display I > don't see any sites in the sequence from chr11:1197789-1197876, but when I > export the DNA sequence using the "DNA" option and specify the "TFBS > Conserved" sites to be underlined, it shows two TFBS sites in this area. > Could you explain? > > > > Thanks, > > > > Max A. > > Max A. Seibold, Ph.D. > Chapman Genetics Fellow > National Jewish Health > Smith Building; A636 > Denver, CO 80206 > Office: (303) 270-2544 > Cell: (415) 505-5156 > [email protected] > > > NOTICE: This email message is for the sole use of the intended recipient(s) > and may contain confidential and privileged information. Any unauthorized > review, use, disclosure or distribution is prohibited. If you are not the > intended recipient, please contact the sender by reply email and destroy all > copies of the original message. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
