[Genome] the meanings of upper and lower cases alphabets in 3'UTR regions of results from the galaxy browser

[Rachel Harte]

Hello Dominik,

We mask repeats in the genome sequence and those bases that are masked are
in lower case. The sequence in upper case is unmasked sequence (no
repeats identified).  Repeats are found with the RepeatMasker program
using repeat libraries from RepBase, and also with the Tandem Repeat
Finder (TRF) program. For the repeats found by TRF, we mask out only repeats
of period 12 or less.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Sun, 3 Dec 2006, Dominik Margraf wrote:

> I got data from the galaxy browser from the hg17 track 3' untranslated
> region exons.  However the sequence I get contains bases in both upper
> and lower cases.
>
> What do the upper case and lower case mean?
>
> Thanks!
>
> Dominik
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