Primate listings in the Table Browser and how to get AA outputs
J. Patrick Malone
At one time, I could use the Table Browser and I would get: Chimp Gorilla Orangutan Gibbon Resus Baboon Marmoset Tarsier Mouse Lemur Bushbaby Now, a few are missing (the prosimians like the tarsier and lemur), though I see from the Genome Browser that Crab-eating macaque,
Green monkey, and Squirrel monkey have been added there. Can we have a complete primate listing in the Table Browser?
There have been some other changes and I need to obtain some explicit instructions or find a work-around of some kind. I am trying
to compare a rather large set of genes (one at a time) from the other primates to human. Previously, I could get an amino acid
sequence, but no matter how I monkey (forgive the pun) with the settings, I can't seem to make that happen. I would like to get the
AAs only because I can then make the web version of BLAT on the site work (these things are huge and your BLAT won't handle them).
I'm open to other options, but I'm somewhat limited. I only have access to Windows 7 and 8 operating systems, so if I were to download
other software and run the sequences on my own machine, it would have to run in a Windows environment, unless there's a way around ?
So,
(1) Can the other primates be added into the Table Browser, or is there another way to make it work?
(2) Since I am often working with really big sequences, how can I get them into a good AA format - if I am to rely on the web BLAT?
(3) If you recommend that I do not use BLAT (I know that there are other options...), is there something that I can use on a Windows
system? If so, since I am looking at several dozen genes, do I need to download every species of interest onto my own machine to run
with the software? It's a big and cumbersome project ... but I know it can be done if I can just work out the details with your amazing
site or some downloadable software.
Thanks for your help!
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Steve Heitner
Hello.
Can you confirm that you are using http://genome.ucsc.edu/cgi-bin/hgTables and not a mirror site? The green monkey and crab-eating macaque genomes only exist on our test server and not on our public site. Even if you were using our test server, the tarsier and mouse lemur genomes do appear there. I also just used the Table Browser to obtain amino acid sequence information and was able to do so without any problems. All of this leads me to believe that you may be using a mirror.
In order for us to know whether or not BLAT would be a good suggestion for you, we would need to know a little more about what you are trying to accomplish. Unfortunately, if our web-based tools are not sufficient, we do not offer command line versions of those tools for Windows.
Please contact us again at gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Steve Heitner
UCSC Genome Bioinformatics Group
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