Dear Kevin, The differences that you are seeing are most likely due to the different versions of RepeatMasker that are being used. In general, successive releases of RepeatMasker and the library that it uses (RepBase Update from http://www.girinst.org) find more and more repeats in genomic sequence.
I hope that this helps. If you have have further questions, please don't hesitate in contacting the mailing list again. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Kevin Gunderson" <[email protected]> To: [email protected] Sent: Friday, August 27, 2010 3:45:24 PM GMT -08:00 US/Canada Pacific Subject: [Genome] Non-conservation of repeat masked sequence between hg18 and hg19 builds To Whom It May Concern: Why isn't repeat masked sequence conserved between hg18 and hg19 builds? Are different repeat masker algorithms used? As an example I have fetched some sequence around SNP rs10493230. Masked sequence (lower case) not conserved between builds rs10493230-Hg18 TCTGGGTCCTTGGAATAGTGTGCTCCTTCCATAGCTGAAATCTTTGGTCCTAGACATAGTCCCTGTACTCTG CAACCACTGATACCATGTTGCTTCCAGTGACCTGGGCTCGGCACCTCTGCATTCCCTCCCTGGGATATCCTA ATGTCTCCCTGAACAGGCACTAGGGAAACAGAAATATCACTCAGACCTATTATTCCAGACATGTCTATACAC ACATATATTATGCTCTCCTAAGGAACAAGGTGCCAAGCCAAATGCAGAACATTCTCTAGAGCCTTGTAGTTA CTCTTCCAAGCAATGCCTAGAGAAGTAGTCTCCAGCTTTCTGTGTTGTTAGGTCCCCTAATACCTGTATGGA TATCTCCATTATTAGTTTCTCTACCCCTTGTCAAGATATGGCTATGTGGCAGGAGGTAGAATGAGAGATTAG TAAGAATCCTGCCATCACATTTCCTCATCTACTTCTTCCTCACTGGAAGCAAATTCCTCTATATCGAATTCT TTCTCCATTAAGACTCACACCTCggccaggcgcggtggcttacgcctgtaatcccaacacttgggaggccaa ggtgggcagatcacaaggtcaggagttcgagaccagcctggccaacatgttgaaacctcgtctctactaaaa atacaaaaattagctggatgtggtggtgggtggctgtaatgccagctactcgggaggctg rs10493230-Hg19 tctgggtccttggaatagtgtgctccttccatagctgaaatctttggtcctagacatagtccctgtactctg caaccactgataccatgttgcttccagtgacctgggctcggcacctctgcattccctccctgggatatccta atgtctccctgaacaggcactagggaaacagaaatatcactcagacctattattccagacatgtctatacac acatatattatgctctcctaaggaacaaggtgccaagccaaatgcagaacattctctagagccttgtagtta ctcttccaagcaatgcctagagaagtagtctccagctttctgtgttgttaggtcccctaatacctgtatgga tatctccattattagtttctctaccccttgtcaagatatggctatgtggcaggaggtagaatgagagattag taagaatcctgccatcacatttcctcatctacttcttcctcACTGGAAGCAAATTCCTCTATATCGAATTCT TTCTCCATTAAGACTCACACCTCggccaggcgcggtggcttacgcctgtaatcccaacacttgggaggccaa ggtgggcagatcacaaggtcaggagttcgagaccagcctggccaacatgttgaaacctcgtctctactaaaa atacaaaaattagctggatgtggtggtgggtggctgtaatgccagctactcgggaggctg Thanks, Kevin Kevin Gunderson, Ph.D. Senior Director, Advanced Research Illumina, Inc. (www.illumina.com <http://www.illumina.com> ) 9885 Towne Centre Dr San Diego, CA 92121 Voice: (858) 202-4591 Email: [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
