Hello, Peng. The RepeatMasker track was created using the RepeatMasker program, created by Dr. Arian Smit. For RepeatMasker-specific questions, I recommend contacting him at http://www.repeatmasker.org.
Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Peng Yu Sent: Monday, May 07, 2012 3:46 PM To: [email protected] Subject: [Genome] Where do the repNames come from? Hi, I see repNames like the following rmsk table. Some names are intuitive (like (CATA)n). But others are not (like Charlie2b). Does anybody know where are these unintuitive names come from? What are the canonical sequence for these repeats with unintuitive names? > head(unique(f$repName),n=100) [1] "L1_Mur2" "(TTTG)n" "Lx9" "RLTR25A" "(TA)n" [6] "L1M2" "B3" "AT_rich" "L1Md_F2" "RLTRETN_Mm" [11] "L1MEf" "RLTR14" "RMER17A" "RLTR13C2" "T-rich" [16] "Lx2" "IAPLTR1a_Mm" "RLTR9C" "ID_B1" "L1Md_A" [21] "(TTC)n" "RLTR1D" "(CA)n" "MER44D" "RLTR13C1" [26] "MER74B" "ID4_" "MLT1A1" "Lx4B" "(TAAG)n" [31] "B4A" "BGLII_B" "(TCTCCC)n" "(TTCTCC)n" "L1_Mur3" [36] "(TTTA)n" "B2_Mm2" "(TTTTTG)n" "B1_Mus1" "(TTCC)n" [41] "Lx7" "L1_Rod" "RLTR45" "RLTR45-int" "PB1D10" [46] "ORR1E" "(CATA)n" "RLTR9B2" "B2_Mm1t" "PB1" [51] "Charlie2b" "(TCTA)n" "(TATG)n" "Lx8" "MTEa" [56] "RSINE1" "(TTTTG)n" "B1F" "L1_Mus3" "MT2_Mm" [61] "(TG)n" "(GAA)n" "L1_Mur1" "RMER4B" "(TC)n" [66] "RLTR10D" "(A)n" "Lx" "(CAAA)n" "MER119" [71] "B1_Mm" "L1Md_T" "(TAAAA)n" "L2a" "(TTG)n" [76] "MTD" "MTC" "U6" "L1M5" "(GAAAA)n" [81] "B1F2" "L1MEg" "Lx5" "L1MB7" "MTEb" [86] "B3A" "RMER15" "RLTR20A" "B1F1" "MLT1A" [91] "(GA)n" "RMER1B" "L1_Mus1" "(CAA)n" "Lx3A" [96] "MLT1B" "MTB" "MLT1C" "L1_Mm" "IAPEY2_LTR" -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
