Good Morning Gu Zhili: The kangaroo rat genome draft scaffolds are constructed from the contigs you found in genbank. We use the draft sequence construction for our genome display and analysis. You can find the draft sequence genome on our download server:
ftp://hgdownload.cse.ucsc.edu/gbdb/dipOrd1/dipOrd1.2bit You can also find the assembled sequence at the Broad Institute: ftp://ftp.broad.mit.edu/pub/assemblies/mammals/kangarooRat/Dipord1.0/ --Hiram guzhili wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
