[Genome] Viewing Orthologs in Genome browser

[Ann Zweig]

Hello Subho,

	It is possible to view orthologous genes in human and mouse, but not in the 
same display at the same time.  But you can easily navigate from one to the 
other using either of these methods.

Method One:
Find your gene in the human genome browser.  Click on that gene to go to the 
details page.  On this page, click on "Other Species".  In this table, click on 
the "Genome Browser" link in the Mouse column.  This will open the mouse genome 
browser to the orthologous gene.  These orthologies between human and mouse are 
computed by taking the best BLASTP hit, and filtering out non-syntenic hits.

Method Two:
Find your gene in the human genome browser.  Turn on the Mouse Net track.  The 
Mouse Net track shows the best mouse/human chain for every part of the human 
genome. It is useful for finding orthologous regions and for studying genome 
rearrangement. In full display mode, the top-level (level 1) chains are the 
largest, highest-scoring chains that span this region.  Click on the top-level 
Mouse Net to go to the details page.  On this page, click on "Open Mouse 
browser" at position corresponding to the part of chain that is in this window. 
  the will open the mouse genome browser to the location of the orthology 
(whether there is a gene there or not).

	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

Please feel free to search the Genome mailing list archives by visiting our home 
page, clicking on "Contact Us", then typing a word or phrase into the search 
box.  On that same page
(http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome mailing 
list.





Subhajyoti De wrote:
> Hi,
>  
>        I am interested in viewing syntenic relationship between my 
> favourite gene and its ortholog in a second species (say mouse). The 
> human gene would be shown along with its neighbouring genomic window 
> (say 10kb) and genes therein. Corresponding mouse gene would also be 
> shown with its neighbouring genomic window and genes therein.
> 
>     Is it possible to somehow show that in the genome browser?
> cheers, Subho
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome