There was similar question recently on this list about mouse ortholog protein sequence comparison: http://www.mail-archive.com/[email protected]/msg03528.html
In your case, if you're searching for protein sequence differences between human and chimp, you might want to start with Ensembl Gene Models, use Biomart.org to download the orthologs, and then compare these with your own scripts. A quick walkthrough on how to get data out of biomart can be found here: http://genomewiki.ucsc.edu/index.php/Gene_id_conversion hope this helps somewhat, cheers Max On Thu, Oct 14, 2010 at 6:53 AM, Brooke Rhead <[email protected]> wrote: > Hello Guy, > > I don't have a good answer for you on whether or not you have missed any > significant references, but one of our engineers suggests that, since > there is a limited number of RefSeq mRNAs for chimp, you might consider > using the Ensembl Genes track for your comparison instead. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Work > > > Tillinghast, Guy, M.D. wrote on 10/12/10 7:12 AM: >> Dear Mary, >> >> Thanks for your reply. I am interested in compiling a list of proteomic >> differences between humans and chimpanzees. I had the impression this >> work had been done before, yet a pubmed search only revealed comparisons >> regarding the kinome (Anamika et al, 2008), and proteases (Quesada et >> al, 2008). >> >> Have I missed any references? >> >> To obtain my list, it appears that I will need to browse the chimpanzee >> genome at the nucleotide level, using human mRNAs as queries. I can do >> this using Bioconductor. Would anyone at UCSC be potentially interested >> in checking my list? Presumably, this effort would result in a >> publication, for which I would be glad to have co-authors. >> >> Guy >> >> -----Original Message----- >> From: Mary Goldman [mailto:[email protected]] >> Sent: Monday, October 11, 2010 8:25 PM >> To: Tillinghast, Guy, M.D. >> Cc: [email protected] >> Subject: Re: [Genome] The Chimpanzee Proteome. >> >> Hi Guy, >> >> The chimpanzee genome is fully sequenced (read the description here: >> http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chimp&db=panTro2), however >> it has not been as intensively annotated as the human genome. Thus, the >> human genome has more mRNAs and protein sequences. >> >> I hope this information is helpful. Please feel free to contact the >> mail list again if you require further assistance. >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> On 10/11/10 5:49 AM, Tillinghast, Guy, M.D. wrote: >>> When I download the complete human proteome from the UCSC browser, I >>> obtain 28998 entries. >>> However, when I employ the same general approach to the Chimpanzee >>> proteome, I obtain only 786 entries. Why this discrepancy? >>> >>> assembly: Mar. 2006 (CGSC2.1/panTro2) >>> track: RefSeq Genes >>> location: genome >>> >>> Has the chimpanzee genome not been fully sequenced? >>> >>> Guy Tillinghast, Newport New, Virginia. >>> >>> >>> CONFIDENTIALITY NOTICE: This e-mail message, including any >> attachments, is for the sole use of the intended recipient(s) and may >> contain confidential and privileged information. Any unauthorized >> review, use, disclosure or distribution is prohibited. If you are not >> the intended recipient, please contact the sender by reply e-mail and >> destroy all copies of the original message. >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> >> >> CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is >> for the sole use of the intended recipient(s) and may contain confidential >> and privileged information. Any unauthorized review, use, disclosure or >> distribution is prohibited. If you are not the intended recipient, please >> contact the sender by reply e-mail and destroy all copies of the original >> message. >> _______________________________________________ >> 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
