[Genome] sequence search

[Hiram Clawson]

Good Morning Dongxian:

Please note the differences in the versions of Mouse you are working with
here.  The NCBI Map viewer is currently showing NCBI Build 37.
The UCSC Genome browser current default mouse display is NCBI Build 36.
You can view the NCBI Build 37 sequence in the UCSC Genome browser.
Go to the gateway browser page,
	http://genome.ucsc.edu/cgi-bin/hgGateway
and select the July 2007 Mouse genome (UCSC mm9)

When you blat your XM_001471686 sequence to the mm9 sequence,
it is found exactly at chr4:155,573,561-155,574,905
Which is contig NT_039268.5

--Hiram

dongxian zhang wrote:
> Hi,
> 
> I am searching the BAC clone information for hypothetical protein  
> XM_001471686 in your Genome Browser.  The search result located the  
> protein to Chromosome 12.  However, the same clone was identified by  
> NCBI Map Viewer in Chromosome 4.  Because this protein matched a  
> genomic contig sequence NT_039268, I used NT_039268 to search your  
> Genome browser.  This time I matched to Chromosome 4.  However, I  
> noticed the sequence number for the beginning and end of NT_039268  
> were different between your and NCBI genome viewer.   Also, if I took  
> the 100K sequence from NT_039268 that contains XM_001471686 to search  
> your Genome Browser using BLAT, I could not match it to chromosome  
> 4.  Could you  explain all these?   How can I identify the right BAC  
> clone that contains XM_001471686?  Your help will be greatly  
> appreciated.
> 
> Sincerely,
> 
> Dongxian
> 
> Dongxian Zhang, Ph.D.
> Associate Professor
> Burnham Institute for Medical Research
> The Neuroscience and Aging Center
> 10901 North Torrey Pines Road
> La Jolla, CA 92037
> USA
> Tel # (858)-795-5263
> Fax# (858)-795-5292
> Web: http://www.burnham.org/default.asp?contentID=194