Hello, Adrian,
You can use the Short Match Track on the Genome Browser
to visualize the locations of a short repeat. Click on
the link in the first track group below the main graphic
and type in the sequence (minimum of 2 bases). This only
works for one sequence at a time.
If you are looking for a file of coordinates (which could
be used as a custom track to visualize), use the Table
Browser.
group: Variation and Repeats
track: Repeat Masker
table (the only choice): rmsk
filter: repName does match: (TGG)n OR (TA)n [for example]
[submit]
output format: selected fields from primary and related tables
then choose the info you desire: genoName, genoStart, genoEnd
will give the coordinates, repName will give the sequence.
[get output]
Here is sample output form this queryon hg19:
#filter: (rmsk.repName = '(TA)n' OR rmsk.repName = 'OR' OR rmsk.repName
= '(TGG)n')
#genoName genoStart genoEnd repName repClass
chr1 16252908 16252959 (TA)n Simple_repeat
chr1 96730871 96731529 (TA)n Simple_repeat
chr1 109313990 109314373 (TA)n Simple_repeat
chr1 112590708 112590862 (TA)n Simple_repeat
chr1 227147684 227147967 (TGG)n Simple_repeat
chr1 16712 16749 (TGG)n Simple_repeat
best wishes, and thanks for using the Genome Browser,
--b0b kuhn
ucsc genome bioinformatics group
On 1/19/2012 10:26 AM, Adrian Johnson wrote:
> Hi:
> Using genomebrowser is it possible to find homopolymer regions in DNA.
>
> I am interested in finding homopolyers of one base of 2 or 3 bases.
>
> Is there a way to find such instances and if not, do you suggest any
> other tool.
>
> thank you in advance.
>
> -Adrian
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
