Hello, Apologies for the delay in replying. The Table Browser will retrieve sequence corresponding to the items in whichever track you have selected. Thus even if you specify a region, the Table Browser returns the sequence for the nearest track item overlapping with your region.
To retrieve sequence for one exact region you can use our getDNA tool (accessible via the "DNA" link in the top bar above the main browser display): http://genome.ucsc.edu/cgi-bin/hgc?g=getDna If you have multiple regions the best thing would be to make a custom track of the regions and then use the Table Browser to retrieve the sequence. For detailed instructions on this method please see this previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2006-September/011647.html Hopefully this resolves the discrepancy from your second question. If not, we will need more information regarding how you obtained each of the conflicting sequences to be able to understand the issue. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu > We have a couple of questions: > > 1) In Table Browser if we request a sequence of a short genomic region of > about 1000bp, Table Browser returns a much longer sequence and the > coordinates are off. Is there any way to retrieve the exact stretch of > sequence that we want? > > 2) We retrieved promoter sequences for TNFalpha from both NCBI sequence > viewer and UCSC Table Browser and they do not match. They are both hg19. > What is the basis for this discrepancy? > > Thank you! > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
