Hello Dr. Iannotti, The first thing to check is that the same version of the genome assembly is being examined. The literature should note the exact genome version in the Methods. The UCSC assemblies note the exact genome version on the Gateway page (http://genome.ucsc.edu/ -> Genome Browser -> set assembly -> genome is named by a short version of the public name and full credits are at the bottom on this gateway page).
If this is not the issue, it may be that the sequence alignment tools used in the publications differ from the tools you are using to map to the UCSC genome or the tools used to create the track (BLAT? keyword search into a track?). The track descriptions at UCSC will have the track Methods explained, which you can compare to the publication's methods. Please note that many species have multiple assemblies available on the main server and even more on the archive server (http://genome.ucsc.edu/ -> Archives). The archive assembly have limited functionality, but it may help you to at least know why the mismatch in results is occurring. Please let us know if you need more help, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/17/10 6:47 AM, [email protected] wrote: > > > Dear Collegues, > > I have been started to use the UCSB database from a week trying to search > a possible consensus regions for the trascriptional regulation factor > (REST called also NRSF or NRSE) on KCNQ4(KQT-like 4) gene, but I'm still > unable to well understand the reason why the consensus regions find using > UCSB database on this gene are mostly different from the canonical ones > described in scientific literature. Can you give me some technical advice > to avoid this gap? > > Region Investigated: KCNQ4(KQT-like 4) gene in mouse Chr 4 > T.F.: REST > C.R.: nnCACGACCnn(nnnn)GGACAGnnnC > > > Thanks a lot in advance for your help. > > Sincerely > > Fabio Arturo Iannotti PhD > Dpt. of Neurobiology, Physiology > and Behavior > University of California > Life Science Building > 95616 Davis CA USA > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
