Hi Seong-il, You can create a fasta format file of protein sequence and mRNA transcript using out table browser.
Click on "Tables" on the blue bar on the top of the main page and make the following selections: clade: Mammal genome: mouse assembly: July 2007 (NCBI37/mm9) group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: genome output format: CDS FASTA alignment from multiple alignment 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 file type returned: plain text Click "get output", and in the page that opens for the mRNA transcript, click "Show nucleotides". Then where you see "Species Selection" click the " - " button (no species will be selected, but mouse will show up). For protein sequence, do all the same steps, just don't select "Show nucleotides". 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. I hope I have answered your question. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group S. Eyun wrote, On 08/27/10 09:15: > Hi, there > > > > I am a graduate student at University of Nebraska. I downloaded mouse genome > sequences at http://hgdownload.cse.ucsc.edu/goldenPath/mm9. However I cannot > find any fasta format protein database. Would you please let me know where > it is? Actually I need the transcript and protein sequences. If you have the > matching table between two databases, just let me know. Thank you so much! > > > > Seong-il > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
