[Genome] UCSC homologene

Brooke Rhead rhead at soe.ucsc.edu
Tue Apr 8 14:14:53 PDT 2008 

Hi Avi,

We only incorporate RefSeq transcripts with identifiers that begin with 
"NM_" into our databases.  We do not include the XP_ and XM_ RefSeq 
accessions.  A description of the different RefSeq accessions is located 
here:

http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accessions

I hope this information is helpful.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Fungazid wrote:
> Hi Ann,
> 
> I'm still contemplating to commit sin ( ;-) ): to use
> the NCBI homologene database. I saw that in the case
> of dog (for example) most genes and their products are
> gene bank predictions like 
> XP_544872.2 	XM_544872.2 
> Can I find cross link to this specific sort of
> annotations in UCSC tables? 
> 
> Many thanks, Avi
> 
> 
> --- Ann Zweig <ann at soe.ucsc.edu> wrote:
> 
>> Hello again Avi,
>>
>> 	We have only created BlastTab tables with pairwise
>> orthologs between the seven 
>> organisms that I listed in my previous email.  Your
>> best bet for viewing the 
>> relationship between the mouse and the dog (or
>> opossum) is to use the Chain/Net 
>> tracks.  In the mouse genome browser, turn on the
>> Chain and Net tracks to the 
>> Dog (or Opossum).
>>
>> 	The Dog Chain track in the mouse browser shows
>> alignments of dog (canFam2, May 
>> 2005) to the mouse genome using a gap scoring system
>> that allows longer gaps 
>> than traditional affine gap scoring systems. It can
>> also tolerate gaps in both 
>> dog and mouse simultaneously. These "double-sided"
>> gaps can be caused by local 
>> inversions and overlapping deletions in both
>> species.
>>
>> 	You can read about the details behind this or 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).
>>
>> 	As for question 2, you are correct: query is the
>> species in this database (in 
>> this case, hg18), and target is the species to which
>> it is aligned (in this 
>> case, mm9).
>>
>> 	The kgXref tables in each database give several
>> aliases for each gene ID.
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>>
>>
>>
>> Fungazid wrote:
>>> 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 
>>>> 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
>>>>  >
>>>>  >
>>>>  >
>>>>  > 
>>>>
> === message truncated ===
> 
> 
> 
>       ____________________________________________________________________________________
> 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

More information about the Genome mailing list