repeat masker

[山田思郎]

Dear webmaster

I always use your website. And it is very excellent. I want to point out one problem.
In your "Repeat Masker" data, there is "Alu detection" error. The same problem had been in CENSOR website also and was fixed now.

Your algorithm detect an "old" Alu sequence as a "new" subgroup AluY.
This is the example:

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RepeatMasker Information

Name: AluYk11
Family: Alu
Class: SINE
SW Score: 317
Divergence: 15.2%
Deletions: 0.0%
Insertions: 0.0%
Begin in repeat: 1
End in repeat: 46
Left in repeat: 266
Position: chr18:55286527-55286572
Band: 18q21.31
Genomic Size: 46
Strand: +
View DNA for this feature (hg19/Human)
View table schema

Go to RepeatMasker track controls

Data last updated: 2009-04-24

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This is the sequence:

>hg19_rmsk_AluYk11 range=chr18:55286527-55286572 5'pad=0 3'pad=0 strand=+ repeatMasking=none
GGCTGAGTGTGATGGCTCACTCCTATAAACCCAGCACTTTGGGAGG

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The result of CENSOR analyses of same sequence is as follows :

Local Alignments*

 
Name
 
From
 
To
 
Name
 
From
 
To
 
Dir
 
Sim
 
Pos/Mm:Ts
 
Score
 
hg19_rmsk_AluYk11
 
1
 
46
 
ALU
 
1
 
46
 
d
 
0.8261
 
1.3333
 
272

1 GGCTGAGTGTGATGGCTCACTCCTATAAACCCAGCACTTTGGGAGG 46
  |||:|:|:|:|:|||||||| |||:||| |||||||||||||||||
1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGG 46


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The studies of Repeats are now becoming increasingly important. And many researcher must use your website for their study. I would like to ask you to fix it.

best regards

Shiro Yamada
National Institute of Genetics
1111 Yata, Mishima, Japan