Hi Tyler, You might also try contacting the authors of RepeatMasker: http://www.repeatmasker.org/ .
Angie On Thu, Jun 7, 2012 at 3:52 PM, Tyler Garvin <[email protected]> wrote: > Hi, > > I have been analysing L1 data from RepeatMasker for mouse (mm9) and I have > been trying to develop an evolutionary tree starting with > L1Md_A/F/F2/F3/Gf/T and backtracking up the tree. From what I have read in > the documentation, UCSC uses some variation of the repeatmasker algorithm > using consensus sequences from Repbase for training the HMM. > > Repbase only has consensus sequences for L1Md_F and L1Md_Gf, however, and > when I align them with the UCSC repeatmasker elements I am finding very > poor similarity between the transposons and their supposed consensus. I > was wondering if you could tell me where to find the training > sequences/procedure that were used to categorize these L1Md elements. In > all honesty, it would be nice if I could have access to these consensus > sequences for all LINE/SINE/LTR elements but I am more focused on the L1Md > elements. > > Thanks, > Tyler > > > -------------------------- > USC Graduate (Fall 2012) > Biomedical Engineering (Electrical) > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
