Hi Andrea, Sorry for my delayed response.
As you probably already know, we don't have the complete Neandertal sequence. On human hg18 assembly, we do have a track called Neandertal Cntgs that shows consensus contigs called (after duplicate reads from each library were merged) from overlapping, non-redundant reads that passed mapping and base quality criteria. For more information about this track, please see the description page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=ntSeqContigs. Because we don't have a Neandertal assembly, we also don't have a Neandertal gene track. However, what I recommend is finding the regions of the ASTN1 and ASTN2 genes on the hg18 human assembly and then getting the contig sequences from our table browser. Please note, the contigs don't cover every base of the human genes and so your sequences will not be fully complete. Here is how you would do this: First, figure out the genomic location of the two genes you are interested in. The easiest way to do this is to turn on the UCSC Genes track in the genome browser. On the main browser page, in the search box labeled 'gene', type your first gene, ASTN1 and click "jump." Click on the transcript you're interested in (to see only the canonical transcript and not the splice variants, click on the gray mini-button on the left of the track image and left of 'Show' un-click 'splice variants', click submit). Once you are looking at the details page of your transcript of interest, record the chromosome position. Do the same for ASTN2. Then go to the Table Browser by clicking on "Tables" on the blue bar on the top of the main page and make the following selections: clade: Mammal genome: Human assembly: Mar. 2006 (NCBI36/hg18) group: Neandertal Assembly and Analysis track: Neandertal Cntgs table: All (bamAll); you can always click "describe table schema" to view descriptions of the table columns. region: click 'define regions' and paste in your two regions & click submit. output format: selected fields from primary and related tables output file: if you would rather have the results saved to a file instead of displaying in the browser window, enter the name you would like the output file to have, otherwise, leave blank Click "get output". Select qName, rName, pos, and seq (and any other fields you're interested in); click "get output." Your results will have the contig sequences and their locations. You'll have to string all the sequences together with your own tools. For more information about using the Table Browser see "Using the Table Browser" by scrolling down past the Table Browser form. It provides brief descriptions of the Table Browser controls. You can also see the "User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Andrea Angueyra Planas wrote, On 5/6/2011 5:34 AM: > Good morning > I am working on a Systematics project, and I would like to extract from your > homepage the nucleotide sequence of two genes of Homo Neanderthalensis, ASTN1 > and ASTN2. Could you help me? > Thank you, and looking forward to your answer, > > Andrea Angueyra > Biology Student > Los Andes University > Colombia, South America > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
