Hm, was just listening, and thought that this file could be useful http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/refMrna.fa.gz ...but I guess from your conversation, that "known mRNAs" is different from "all mRNAs in Genbank"... ?
cheers Max On Thu, Mar 4, 2010 at 12:41 AM, Brooke Rhead <[email protected]> wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
