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
