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]
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