Greg, Thanks a ton for those directions, but I have one issue: at the bottom of the output using the steps below (as well as selecting gzip) this is what I get carefulAlloc: Allocated too much memory - more than 6,442,450,941 bytes (6,442,456,810)
Sorry to be such a burden, and hopefully this isn't too trivial. I actually think these are probably in the major databases considering there are 219 entries in Swiss-Prot <http://www.uniprot.org/taxonomy/9685>, and 231 in Ensembl <http://useast.ensembl.org/Felis_catus/Info/StatsTable?db=core>. Still it would be nice to at least confirm we are working with the most up to date. Thanks again, Ben On Mon, Apr 11, 2011 at 8:09 PM, Greg Roe <[email protected]> wrote: > Hi Benjamin, > > You can use the table browser to get the data. From the Genome Browser home > page, select Tables from the top menu and: > > Select (Clade/Genome/Assembly) > Mammal/Cat/felCat4 and: > > group: Gene and Gene prediction tracks > track: refSeq Genes (or one of the other gene sets) > table: refGene > region: genome (or select position to get a sequence for a specific region) > identifiers (names/accessions): if applicable, click on "paste list" and > paste in the identifiers following the instructions. > output format: sequence > Click get output > > Select sequence type: genomic > Click Submit > > On the sequence retrieval options page, uncheck all boxes except CDS Exons. > Then click Get Sequence. > > I'm not sure what version of the cat genome is currently hosted at Ensembl > or UniProt. I do know Ensembl does host a cat genome. Our felCat4 = > NHGRI/GBT V17e. > > If you have any additional questions, feel free to contact us again at: > [email protected] > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > > -------- Original Message -------- >> Subject: Protein FASTA of GTB V17E assembly (December 2008, UCSC >> version felCat4) >> Date: Mon, 11 Apr 2011 13:23:41 -0400 >> >> I am currently doing some proteomic analysis of Felis catus samples and >> was making sure I had the most current protein database. Is the felCat4 >> release included in public databases such as UniProt or Ensembl, and >> more specifically, do you have a CDS translated fasta of felCat4 >> available? I have looked on various websites and couldn't find this, >> which is why I am emailing your group. If there is someone else I should >> ask about this, I appreciate any help in directing me to them. >> >> Thank you for your time, >> Benjamin Neely, Ph.D. >> Post-doc >> Nephrology Proteomics Laboratory >> Medical University of South Carolina >> Charleston, SC, USA >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
