[Genome] small caps in genome

[Kayla Smith]

Hello Vesko,

I am assuming that you are using the Table Browser to retrieve sequence 
information.  You will notice in the Sequence Retrieval Region Options 
that there are some formatting options.

Sequence Formatting Options:
-Exons in upper case, everything else in lower case.
-CDS in upper case, UTR in lower case.
-All upper case.
-All lower case.
-Mask repeats: to lower case to N

The answer to your question will depend on which buttons you have 
checked in the output options.

Another time that you will see upper and lower case letters is when 
looking at repeat masked sequence.  In that case generally repeatmasked 
sequence is in lower case.

In addition, please see this previously asked (by you) mailing list 
question:
https://www.soe.ucsc.edu/pipermail/genome/2008-April/016200.html


I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group.

Vesselin Baev wrote:
> Dear All,
> I gave extracted via BED file sequences from PanTro2 genome, and I have
> simetimes small caps letters- what they mean?
> 
> 
> 
> 
> Vesko
>