Hello, If the EST is included in one of the UCSC tracks, you can retrieve the alingment coordinates from the Table Browser. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser
If the EST is not included in one of the UCSC tracks, then BLAT the sequence against genomic, export/save the results and/or keep as a custom track. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign Try these tools and please let us know if you need additional help, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "James E Zadina" <[email protected]> wrote: > From: "James E Zadina" <[email protected]> > To: [email protected] > Sent: Saturday, August 29, 2009 8:37:09 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Chrom coordinates of sub-sequence within an EST > > I have a collection of ESTs that contain a short target sequence I am > interested in. > > Most of them can be matched to chromosome coordinates that have a > matching genome sequence, but several do not, indicating that they > are > either mis-sequenced or may be spliced within the target sequence. > > Is there a way to query (preferably in batch mode) for the chromosome > coordinates of a sequence within an EST? > > > > For example, if an EST has a length of 1000 and I know my target > sequence is at position 408-468 within the EST, but because of > introns, > the length of the EST on the chromosome is much longer than 1000. Is > there a way to structure a query with the EST accession numbers and > target positions and get chromosome coordinates for the targets only? > > > > > Thanks > > Jim > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
