Hi Rodney, I'm sorry but I could not get your link to work. We recommend using Sessions to show us or another user what you are seeing in the browser (for more information see: http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html).
I looked at chr9:86618860-86619360 on hg18 and see that though the chain/net track indicates that this is homologous to a section of chromosome 13 in mm9, however, when you blat the DNA from this region onto mm9 it does not map to the same region. One of our developers had this to say: "It looks like the flanking region has a lot of base differences between human and mouse, and the human 500bp sequence seems to be rather low complexity with a lot of T's, but not low enough complexity for Tandem Repeat Finder to call it low complexity. The chains have a tendency to blast through regions that don't align really well if they are flanked by higher scoring alignments. It could be that the 500bp region is not actually in mouse." I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 2/15/11 2:04 PM, Rodney Perry, Ph.D. wrote: > I have compared a human gene to the mouse homolog. In one particular > area of the gene, the chained alignment and net alignment appear to show > the sequence around a particular human SNP is present in the mouse, i.e, > it is green. However, when I try to blast the sequence on NCBI, I > retrieve no mouse sequence around the SNP but I do retrieve sequences > upstream. Can you explain the discrepancy? The link to the sequence on > the browser is below. > > > > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr9:86618860-86619360&; > hgsid=186338471&snp130=full&hgFind.matches=rs1624327, > > > > > > Thank you for your assistance in this matter. > > > > Rodney P. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
