[Genome] question about UCSC STS
Anyuan Guio
aguo at vcu.edu
Fri Oct 5 15:16:38 PDT 2007
Dear colleague,
Thank you for your excellent work on UCSC genome browser. But now I
have a question about it.
I find the physical location of some STS markers on UCSC are not
consistent with the NCBI UniSTS.
Such as marker AFM280ZA5 (alias D1S469), the location start at
221008275 and end at 221008670 on chr 1 on UCSC
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=98338741&o=221008274&t=221008670&g=stsMap&i=AFM280ZA5&c=chr1&l=220908274&r=221108670&db=hg18&pix=620
But the same marker is located from 221008331 to 221008659 of chr 1
annotated on NCBI UniSTS
(http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=65827).
I noticed that the NCBI current human assembly version is Build
36.2. However this Build 36.2 is identical to build 36.1 as NCBI release
notes described.
(http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html)
And the UCSC human genome version is Human Mar. 2006 (hg18)
assembly, based on the NCBI Build 36.1 as described on
http://genome.ucsc.edu/cgi-bin/hgGateway.
So, the two human genome assembly is the same, but a STS marker
located on different physical location on UCSC and NCBI. Why? Which can
I used?
Thanks very much!
Anyuan Guo
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