[Genome] 'orthologs' matches

[Brooke Rhead]

Hello Matteo,

Since the time the answer you linked to was written, we have added a new 
feature to the xxBlastTab tables:  we now filter out non-syntenic hits 
between human, mouse, and rat.  So perhaps the hg18.mmBlastTab and/or 
mm9.hgBlastTab tables would be useful to you as-is.

The description of the xxBlastTab tables can be found in the "Other 
Species" section of the UCSC Genes page (this page, and the other 
species columns in the Gene Sorter, is where the contents of those 
tables are actually displayed in the Genome Browser):

"Orthologies between human, mouse, and rat are computed by taking the 
best BLASTP hit, and filtering out non-syntenic hits. For more distant 
species reciprocal-best BLASTP hits are used. Note that the absence of 
an ortholog in the table below may reflect incomplete annotations in the 
other species rather than a true absence of the orthologous gene."

Regarding your question about blastToPsl, there are many blast-type 
formats, and blastToPsl only works with some of them.  If you would like 
to send us a few sample lines of megablast output, we can add that 
format to the list of formats that we want blastToPsl to support. 
(Although it might take some time before we add support for it.)

I hope this information is helpful.  If you have further questions, 
please do not hesitate to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Matteo Re' (matteo.re) wrote:
> Hello,
> 
> I'm trying to find the "most probable" orthologs alignment between
syntenous genomic regions of human and mouse. In presence of clustered
gene families (such as the HOXA cluster) a (say) human
> region can be covered by more than one alignment. My goal is to find
the most probable ortholog match . I've read about a similar problem in
this post
> 
> http://www.soe.ucsc.edu/pipermail/genome/2006-March/010178.html
> 
> but the proposed solution is suitable for entire transcripts using as
> 
input the RefSeqAli table content. I've also tried to convert our
aligner (MEGABLAST) output to psl format (using blastToPsl) in order to
process the output as suggested in the aforementioned post but i was
unable to obtain the format conversion.
> 
> There is a way to translate the megablast output to psl format?
> 
> I'm new to ucsc genome tools, so I'm sorry in advance for the naive
question.

> 
>    Matteo
> 
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