[Genome] question/mistake?

[Robert Kuhn]

Dr. Kozak,

Thanks for using our site.  We are aware of the human chrom 2
color issue. This is an artifact of a change made by the 
sequencing consortium responsible for the chimp assembly.
Beginning with the chimp assembly we call panTro2, they have 
chosen to renumber the chromosomes formerly called chr12 and 
chr13.  These are now called a more human-centric chr2a and 
chr2b, so they appear as the same color in the browser and 
on the page you site.  

There has been some discussion within our group about how to make
the display more graphically represent the situation, but we have 
not yet implemented any such change.  

On the previous human assembly (our hg17), which has alignments to 
the prevous chimp assembly (panTro1), the color difference is
clearly visible.  

compare:

hg17:
http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg17_chr2_chimp
hg18:
http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_chr2_chimp

We're sorry for any confusion this may have caused.

best wishes,

			--b0b kuhn
			ucsc genome bioinformatics group


> From genome-bounces at soe.ucsc.edu  Mon Jun  4 09:03:59 2007
> To: <genome at soe.ucsc.edu>
> Subject: [Genome] question/mistake?
> 
> http://www.cbse.ucsc.edu/research/research_human_chimp_mouse.shtml
> 
>  
> 
> This chart on your website shows the blocks of conserved synteny in
> human and chimp.  It has been shown that two chimp chromosomes fused to
> form human chromosome 2.  So human chromosome 2 should have two blocks
> of color corresponding to two chimp chromosomes.  Also, chimps should
> have 1 more chromosome than humans.  
> 
>  
> 
> Christine Kozak, Ph. D.
> 
> Viral Biology Section
> 
> LMM, NIAID, NIH
> 
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