[Genome] mouse-human orthologs from genome alignments

[Rachel Harte]

Hello Avril,

The mmBlastTab does indeed have best Blastp matches between the proteins
for the human Known Genes set and the proteins for the mouse Known Genes
set. The problem with the Blastp set is that it include orthologs and 
paralogs. Another problem is that proteins that are mostly just a single 
domain could be matched to other proteins only because they share the 
domain and have high levels of identity in this region. In this way, 
paralogs could be matched instead of orthologs using this method.

The nets are the best alignments to use for finding orthologs between 
species. The mouse net for the human genome has the best mouse match for 
each region of the human genome. The reverse is true for the human net for 
the mouse genome. It sounds like the method that you outlined below would 
work fine for finding the mouse-human orthologs using the net files.
You might find it helpful to use out pslMap program:
usage:
    pslMap [options] inPsl mapFile outPsl

This program can take a psl file e.g. the refSeqAli table for human, and 
using the mouse chains for human as the mapFile, you can map the positions of 
the human mRNAs to the mouse genome.  This program is available in our 
source code:

http://hgwdev.cse.ucsc.edu/FAQ/FAQlicense#license3
pslMap is in the kent/src/hg/pslMap directory.

I hope that this helps you. Please let us know if you have further 
questions.

Rachel

On Tue, 28 Mar 2006, Avril Coghlan wrote:

> Hello,
>
> I am wondering whether you have a list of human-mouse orthologs
> that are inferred from the human-mouse genome alignment?
>
> As far as I can see, the human-mouse orthologs given in the Table
> Browser  (mmBlastTab table) are derived from best blast matches
> (and not from the human-mouse genome alignment), is that right?
>
> I would like to infer human-mouse orthologs from the genome alignment,
> and am not sure if this information is already stored in the UCSC
> genome browser, or download files.
>
> So far I've figured out a way to do this is:
> (i) find the coordinates of human and mouse genes from the Table Browser
> (ii) for each human gene X, use the hg17.mm7.net file to find
>     the mouse region M1 that aligns best to the human region H1
> containing
>     gene X
> (iii) use the hg17.mm7.all.chain file to find which bases in the mouse
>     region M1 are aligned to human gene X in human region H1
> (iv) see which mouse gene Y is found in the mouse bases that align
>     to human gene X
> Does this sound right? Is there an easier way to infer human-mouse
> orthologs from the genome alignment? I understand from the paper
> Kent et al 2003 'Evolution's cauldron' that you have inferred
> human-mouse
> orthologs from the genome alignment before, am I doing it the right
> way?
>
> I'm new to the UCSC genome browser (which I'm finding very nice)
> so I'm sorry in advance if this is a silly question.
>
> regards
> Avril Coghlan
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>

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