Hi Gu, The individual that can answer your question is unavailable until next week. We will respond to your question sometime next next week. Thank you for your patience.
Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: guzhili <[email protected]> Date: Mon, Nov 21, 2011 at 6:22 PM Subject: [Genome] A question about the pairwise alignments between human and kangaroo rat To: genome <[email protected]> Dear staff members, We are from CAS-MPG Partner Institute for Computational Biology, Shanghai, China. Nowadays, we are doing a project about Kangaroo rat. Your database have helped us a lot for our work, but there's still a problem made us very confused. The problem is: some scaffods in the pairwise alignments between human and kangaroo rat cannot be found in the kangaroo rat genome. For example, we downloaded the pairwise alignments between human and kangaroo rat from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsDipOrd1/. In the first lines of the file "chr1.hg19.dipOrd1.net.axt", we can see : 0 chr1 12177 12243 scaffold_163392 995 1061 - 3781 But actually we cannot found scaffold_163392 in the kangaroo rat genome. The kangaroo rat assembly ,which is dipOrd1, Jul. 2008, Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000), can be found in Genebank. (http://www.ncbi.nlm.nih.gov/genome/?term=ABRO01&submit=Go and http://www.ncbi.nlm.nih.gov/nuccore?term=EQ846228:EQ921757[PACC] ). We are looking forward to your replay. Gu Zhili 11.11.22 P.S. Sorry for my poor English. ^_^ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
