[Genome] UCSC homologene

[Ann Zweig]

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 
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.


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
 >
 >
 >
 > 
____________________________________________________________________________________
 > You rock. That's why Blockbuster's offering you one month of 
Blockbuster Total Access, No Cost.
 > http://tc.deals.yahoo.com/tc/blockbuster/text5.com
 > _______________________________________________
 > Genome maillist  -  Genome at soe.ucsc.edu
 > http://www.soe.ucsc.edu/mailman/listinfo/genome