Hi Kelson, RepeatMasker is a pretty complex tool -- it begins with alignments of those RepBase sequences, but then does quite a bit of post-processing. Some repeat annotations in the output of RepeatMasker are stitched together from alignments of multiple library pieces, for example "L1_Mur2" appears in the output but the RepBase library has sequences L1_Mur2_5end and L1_Mur2_orf2. I believe RepeatMasker applies many heuristics such as evolutionary history of repeat families and the GC% composition of the local genome sequence. I haven't used queryRepeatDatabase.pl, so can't comment on that at all, but the ultimate authority on RepeatMasker would be the authors:
http://repeatmasker.org/ Hope that helps and please let us know if you have more questions about the Genome Browser tools and tracks, Angie ----- "Kelson Zawack" <[email protected]> wrote: > From: "Kelson Zawack" <[email protected]> > To: [email protected] > Sent: Tuesday, January 18, 2011 1:28:34 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Getting the Repeat Consensus Sequences Used by Repeat Masker > > I am trying to get the consensus sequences of the mouse repeats > annotated in the RepeatMasker track for assembly mm9. Origionally I > just downloaded the most recent set of mouse repeat consensus sequences > from RepBase, but the names by and large don't match up with those in > the RepeatMasker track. I then tried downloading the RepeatMasker > database and using the queryRepeatDatabase.pl utility provided with > RepeatMasker, but it only returned a list of simple repeat names, and > even these did not include the actual sequences. Where can I go to get > the consensus sequences of the repeats annotated in the RepeatMasker mm9 > track? > > Thanks for your help > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
