Hi Kerry, Thank you for the offer, but since we don't have plant genomes our site it probably isn't the best place to post it. However, there is a newer Arapadopsis mirror at Dartmouth (link below) that we just added to our list of other mirror sites yesterday that might be interested in posting it. I would suggest contacting them.
http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/26/11 10:17 AM, Kerry Bubb wrote: > I guess I was hoping that you guys would run LiftOver and provide the > over.chain files for Arabidopsis, as you do for the other organisms (eg: > Elephant and Opossum), but I could run it myself. Since I don't think there > is another place where this translation information is available, if I make > the over.chain file, would you post it on your website? > -Kerry > > On Thu, Aug 25, 2011 at 3:57 PM, Vanessa Kirkup Swing > <[email protected]>wrote: > >> Hi Kerry, >> >> Please take a look at this previously answered mailing list: >> >> https://lists.soe.ucsc.edu/pipermail/genome/2010-January/020985.html >> >> Also, here is a list of mirror sites that may be of interest to you: >> >> http://genomewiki.ucsc.edu/index.php/Other_genome_browsers#Other_genome_browsers >> >> Hope this helps! If you have further questions, please don't hesitate >> to contact the mailing list: [email protected]. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ---------- Forwarded message ---------- >> From: Kerry Bubb<[email protected]> >> Date: Thu, Aug 25, 2011 at 11:16 AM >> Subject: [Genome] Arabidopsis >> To: [email protected] >> >> >> Hello! >> >> I am interested in converting coordinates between releases of the plant, >> Arabidopsis thaliana. I can't seem to find a generally used tool for this >> in the plant community, so I would like to use your LiftOver tool, but I >> don't see an over.chain file for Arabidopsis. I realize that the main >> thrust of UCSC is not plants (I believe there are none on your main >> download >> page), but since it is such an analogous situation, it may be easy for you >> to generate the Arabidopsis LiftOver files. >> >> If you are willing to generate these files, I can provide better pointers, >> but as a starter, Arabidopsis genome sequences are available at TAIR: >> ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/ >> >> Thank you very much! >> -Kerry >> _______________________________________________ >> 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
