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

[Dominik Margraf]

Hi!

Here what do you mean for "repeat"?  Do you mean sequence that occur
(conserved) in more than one place or sequence in a entry overlap with
another enty?

Now I am investigating conserved motifs in non-coding RNA and I
downloaded all the 3'UTR, then I found some of these sequences have
some lowercase sections within some of the 3'UTRs e.g.

GACAGAAATCAGTAatatttatatAGT....

Then should I ignore the lower case parts or should I just treat the
lower case parts same as upper case part?

Thanks!

Dominik


2006/12/3, Rachel Harte <hartera at soe.ucsc.edu>:
> 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
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> >
>