Hi Chris, Unfortunately, the searching issue is a known bug and is on our long list of things to get to. If you have the coordinates, you can get to the annotation pages by having the Old UCSC Genes track ( http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr2&g=knownGeneOld5) visibility set to "full" and the click on the gene of interest to get to the genes detail pages.
If you don't have the coordinates, the table browser ( http://genome.ucsc.edu/cgi-bin/hgTables) can be used to get the coordinates. After selecting the appropriate clade, genome, and assembly set the following: group: Genes and Gene Prediction Tracks track: Old UCSC Genes table: knownGeneOld5 region: genome identifiers (names/accessions): paste in your list of identifiers output format: hyperlinks to Genome Browser Click "get output" This will provide you with links to each of your identifiers in the browser. You will need to click on the identifier in the browser image to get to the details page. If you aren't familiar with the table browser, please see the following for help: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/cgi-bin/hgTables#Help To get you started here is the details page for uc002vnm.2: http://genome.ucsc.edu/cgi-bin/hgc?db=hg19&o=224461659&t=224467121&g=knownGeneOld5&i=uc002vnm.2 Sorry for the inconvenience! If you have further questions, please email the list: [email protected] Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Chris Bizon <[email protected]> Date: Tue, Mar 13, 2012 at 10:29 AM Subject: [Genome] older transcript versions To: "[email protected]" <[email protected]> Hi, I'm looking at some precomputed polyphen-2 results, and they have been computed against particular versions of the known genes tables. However, those versions are no longer the most current versions (at least in some cases). Is there a way to pull the actual mRNA or protein sequence for an older version of a transcript? For instance, searching for uc002vnm.2 through the website will only find uc002vnm.3. The annotation download page has a knownGeneOld5, which does include the older accession number, but no actual sequence. Thanks, Chris Bizon Senior Informatics Scientist Renaissance Computing Institute UNC-CH _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
