[Genome] UCSC homologene

[Fungazid]

Ann, 
thank you for your nice help, I must say .I have
another 2 related questions (I hope it is not too
detailed )

1)
what do you mean by: "For more distant 
species reciprocal-best BLASTP hits are used." ?? For
example how can I find the target gene of dog or
opossum, for a query mouse gene?

2)
About the mmBlastTab table in hg18 database: 
As far as I understand:
a.	'query' field = the name of human gene, 
b.	'target' = the name of the homologous gene is mouse
c.	hg18 and mm8 kgXref  tables give aliases to the
query and taget gene names respectively.
I hope this is right

Thank you again, Avi


--- Ann Zweig <ann at soe.ucsc.edu> wrote:

> Hello Avi,
> 
> 	We have several data sets available that show
> homologous genes.
> 
> 	The BlastTab tables show pairwise orthologs between
> the following 
> organisms:
> 
> organism	tableName
> --------	---------
> human		hgBlastTab
> mouse		mmBlastTab
> rat		rnBlastTab
> zebrafish	drBlastTab
> D. melanogaster	dmBlastTab
> C. elegans	ceBlastTab
> S. cerevisiae	scBlastTab
> 
> 	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.
> 
> 	The Conservation tracks show multiple alignments of
> a number of species 
> along with measures of evolutionary conservation. 
> For example, the 
> Conservation track on the latest human assembly
> (hg18), shows alignment 
> with 27 other vertebrates.
> 
> 	You can read about the details behind any track
> (description, methods, 
> display, credits, references) by pressing on the
> 'mini-button' to the 
> left of the actual track display, or by clicking on
> the hyperlinked 
> track name in the track controls (below the
> display).
> 
> 	You can use the Table Browser tool on our website
> ('Tables' from the 
> top blue navigation bar) to view the contents of
> tables.  Alternatively, 
> you can download tables from our download sever
> here: 
> http://hgdownload.cse.ucsc.edu/downloads.html
> 
> 	This should be enough to get you started.  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 
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> 
> 
> Fungazid wrote:
>  > I would like to ask 2 questions:
>  >
>  > 1) Is there UCSC-tables that group homologous
> genes ?
>  > More specifically, tables that group together
> genes
>  > that their conservation is measured at the
> protein
>  > level, or mRNA level.
>  > for example, the table should look like:
>  >
>  > groupNumber gene species
>  > 1 NM_001011874 mm8
>  > 1 NM_001011971 rn4
>  > 1 NM_052898 gh18
>  > ...
>  >
>  > + some conservations measures
>  >
>  >
>  > 2) There are similar tables in homologene
> database:
>  >
>  >
>
http://www.ncbi.nlm.nih.gov/sites/entrez?db=homologene&cmd=search&term=
>  >
>  > Is there a way to link these tables to UCSC
> refGene
>  > tables, or similar UCSC gene tables?
>  >
>  > Many thanks, Avi
>  >
>  >
>  >
>  > 
>
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>  > Genome maillist  -  Genome at soe.ucsc.edu
>  > http://www.soe.ucsc.edu/mailman/listinfo/genome
> 



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