[Genome] [Fwd: A query on the Genome Browser]

[Ann Zweig]

Hello Siddarth,

	In the genome browser and the associated tools, much of the upper- and 
lower-case display is controlled by the user.  When you ask for DNA sequence 
output using most tools (Table Browser, 'DNA' link, etc.) the case is 
configurable.  So this inconsistency may be a simple factor of your having two 
views configured differently.

	When you retrieved the output from the Table Browser, you must have chosen a 
gene set from which to extract the exonic sequence (e.g. RefSeq Genes, UCSC 
Genes, etc.).  I note that in the particular location you mention 
(chrM:6903-7445) there is a UCSC Gene, but not a RefSeq Gene.  This could be 
causing the inconsistency you are seeing.

	In the future, please direct your questions to the genome mailing list at 
genome at soe.ucsc.edu -- our moderated forum for user questions and discussion. 
You will likely get a quicker response to your question.

	I hope this information is helpful to you.  If this has not fully addressed 
your issue, please contact the list again with further details and a list of the 
exact steps you have taken to see the inconsistency.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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> -------- Original Message --------
> Subject: 	A query on the Genome Browser
> Date: 	Mon, 31 Dec 2007 16:44:27 -0700
> From: 	SiddarthGautham Selvaraj <sselvar1 at asu.edu>
> To: 	cbseweb at cbse.ucsc.edu
> 
> 
> 
> Respected Sir:
> 
> I am Siddarth Gautham Selvaraj, a graduate student in Arizona State 
> University. My interest lies in collecting all the coding exons in the 
> human genome with its homologs.
> 
> I used Table browser to get the sequences of all codig exons for each 
> chromosome. An interesting fact which I found out and could not 
> understand is that why not all coding exons mentioned by the Table 
> Browser not capitalized n the genome browser window. I find for example 
> in chromosome M sequence in position 6903-7445 as coding exons in Table 
> Browser but the same sequence is not capitalized which means is not 
> considered coding by the genome browser. I found very difficult to 
> understand this concept.
> 
> Also what exactly is the capitalized coding regions put by the genome 
> browser?
> 
> Thanks
> siddarth