Hi Ken, You can obtain the sequence of the entire UCSC Genes track (or any portion of it) from the Table Browser (click on "Table" in the blue bar).
>From your attachment, I can see that you are using the most recent mouse assembly (July 2007) and so these instructions will help you get the sequence for the UCSC Genes track on that assembly. You will end up with a plain text file of the UCSC Genes track sequence for each chromosome (there is too much information to have the entire genome in a single file). Therefore, you will need to repeat the steps below for each chromosome. After completing these steps for chromosome 1, replace "chr1" in the position field with the next chromosome until you have completed these steps for each chromosome. Each of the output files will contain the sequence of each gene that is located on that particular chromosome, in order (each gene is preceded by a brief header that starts with ">"). Once you have the Table Browser open, set the following parameters: clade: mammal genome: mouse assembly: July 2007 group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: position; type "chr1" in the field next to position output format: sequence output file: enter the name you would like the output file to have (e.g. chr1KnownGeneSeq) file type returned: plain text Click "get output." Select "genomic" and click "submit" On this page, you can select which parts of the genes (including flanking regions, if you wish) and you can make some adjustments as to how you want the data to be displayed. Click "get sequence" Repeat for each chromosome. I you have any further questions, please contact us. Katrina Learned UCSC Genome Bioinformatics Group Osaki, Ken wrote: > Hello there, > > How can you download the entire dataset of UCSC Gene Prediction's > sequences? > What I'm talking about is what you see the top sequence(s) in the Genome > Browser (two Frap1 seqs in my attached file). > If there are separtate dataset of these Prediction sequences, not include > other Refseq, Ensembl, or EST, please tell me where I can download the > dataset. > > Regards, > Ken > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
