Hi Adrian, I'd like to mention one more track in the Variation and Repeats group that is more specific to tandem repeats: Simple Repeats. In the table browser, after selecting the Simple Repeats track, you can create a filter with period <= 3 which will return repeats with repeating sequences of 1, 2 or 3 bases. They may not be completely pure since the algorithm tolerates some divergence (as does RepeatMasker I think), but you can get some idea of how pure they are from some of the fields such as A, C, G and T counts.
Angie ----- Original Message ----- > From: "robert kuhn" <[email protected]> > To: "Adrian Johnson" <[email protected]> > Cc: [email protected] > Sent: Thursday, January 19, 2012 11:32:58 AM > Subject: Re: [Genome] finding polymer region > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
