Hi Shobha, There are a couple of ways to do this. The first is to use the Table Browser (the "Tables" link in the blue bar at the top of the page). Select the UCSC Genes track and region "genome", then "output format: sequence". Enter a name for the output file. You will likely want to select the "gzip compressed" option, as this will generate a somewhat large file (170M as plain text, 33M compressed). On the next page, select "mRNA", then hit submit.
Another option is to download the table 'knownGeneMrna', which contains the same sequence data (it is rather odd for sequence in the Genome Browser to be stored in a table, but this one is an exception). It won't be in fasta format exactly, but it will be close. The download is available from the "Annotation Database" link under hg18 on our downloads page (http://hgdownload.cse.ucsc.edu). Here is a direct link: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGeneMrna.txt.gz or you can get it with ftp from the same location: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGeneMrna.txt.gz I hope this is helpful. -- Brooke Rhead UCSC Genome Bioinformatics Group On 03/03/10 05:24, Shobha Potluri wrote: > Hi, > I am interested in obtaining a fasta file containing all > cdna sequences from the hg18 annotation. One way to do this would be > to extract the transcript starts and ends from the knownGene table and > extract the corresponding sequences. > > Is there an easier way to obtain this information? > > Kindly let me know. > > Thanks, > Shobha. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
