how to find categorized satellites

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9.5 years ago

R ▴ 10

Hi,

I would like to categories satellites into major and minor mouse ? in repeat masker file which I downloaded from UCSC only mentioned satellites and nothing more!

Thank you very much

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ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by R ▴ 10

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R, what you mean by minor and major satellites (can you give examples)?

ADD REPLY • link 9.5 years ago by PoGibas 5.1k

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In the mouse, Mus musculus, two types of repetitive DNA sequences are associated with centromeres. These are the major satellite repeats (6 megabases of 234 bp units) and minor satellite repeats (∼600 kb of 120 bp units)

ADD REPLY • link 9.5 years ago by R ▴ 10

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Doesn`t repeat masker has repeat family and repeat class fields? I guess it`s possible to get what you want through those fields.

ADD REPLY • link 9.5 years ago by PoGibas 5.1k

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No, it does not categorize them

ADD REPLY • link 9.5 years ago by R ▴ 10

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R, these 2 groups were classified 17 years ago and I am not surprised that you can't find equivalent groups for them in current Repeat Masker release. Current Repeat Masker classification is based on sequence similarity.

My suggestion would be to extract all satellites from UCSC Repeat Masker (repClass = Satellite) and try to figure out which have characteristics similar to those mentioned in this paper.

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by PoGibas 5.1k

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