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
