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

[Hiram Clawson]

Good Evening Dominik:

You can read about Repeat Masker and what it is marking at:
	http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=rmsk
	http://www.repeatmasker.org/
which uses RepBase:
	http://www.girinst.org/repbase/update/index.html

Depending on the purpose of your investigation, you can ignore
the repeat masking.

--Hiram

On 2006 Dec 02, , at 6:46 PM, Dominik Margraf wrote:

> 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
>>>
>>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>