[Genome] Stumped

[Ann Zweig]

Hello Kateri,

	As you probably noticed in the "Cat Chained Alignments" track on the 
human assembly, all you see are scaffolds (not chromosomes).  This is 
because the entire cat assembly (felCat3) is still on scaffolds; that 
is, it has not yet been assembled onto chromosomes.

	You may be able to find more information about the cat genome on these 
sites:

http://home.ncifcrf.gov/ccr/lgd/comparative_genome/catgenome/index_n.asp

GARfield browser: http://lgd.abcc.ncifcrf.gov/cgi-bin/gbrowse/cat/


	I hope this information is helpful to you.  Please don't hesitate to 
contact the mail list again if you require further assistance.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




McCarthy, Kateri (NIH/NICHD) [F] wrote:
> To Whom It May Concern:
> 
>  
> 
> I have a question and I don't know if you might be able to help me out.
> I am trying to find homologies between pseudoautosomal-region genes on
> the X chromosome to the cat.  I'm using "Cat Chained Alignments" but I
> am concerned I don't see a chromosomal position for the scaffolds that
> are aligning.  I would hope the homologs on the cat are located on the
> cat's X chromosome - but I can't seem to find a chromosome position.
> How can I determine the chromosomal position on the segments that are
> aligning to the human X chromosome gene?  For example, I am aligned CD99
> using the Cat Chained Alignment (I CAT Blat'ed the human CD99 sequence
> to get a quantitative sense of its alignment) - but how do I know where
> it's located?  My assumption is that it should be on the cat's X as
> well.
> 
>  
> 
> I hope you understand the problem.  If you can offer any assistance I
> would be very grateful!
> 
>  
> 
> Thank you for your time,
> 
>  
> 
> Kateri 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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