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mm9 repeat seq coordinates

Is there any database which can give me repeat sequence coordinates in mm9. I know repeatmasker can do this but trying to find if there are already such seq coordinates are summarized to filter my data.

Thanks

mm9 repeat-sequence
• 3,712 views • link
updated by Ram Ram • written by kanwarjag kanwarjag

Thanks Ashutosh,

When I read the properties of the bed file generated-

Display Conventions and Configuration

In full display mode, this track displays up to ten different classes of repeats:---

  • Short interspersed nuclear elements (SINE), which include ALUs
  • Long interspersed nuclear elements (LINE)
  • Long terminal repeat elements (LTR), which include retroposons
  • DNA repeat elements (DNA)
  • Simple repeats (micro-satellites)
  • Low complexity repeats
  • Satellite repeats
  • RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
  • Other repeats, which includes class RC (Rolling Circle)
  • Unknown

As per above description , it will out put repeat regions, which I may want to exclude. However, when I use above filter- there are 4989421 rows (coordinates) it appear that it is filtering out repeat mask coordinates and out put coordinates with above regions (repeat etc). Am I missing something?

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updated by Ram Ram • written by kanwarjag kanwarjag

Hi Kanwar, I didn't quite get what you meant above. It has been a long day for me :-) Can you elaborate or rewrite the last three lines. Thanks.

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updated by Ram Ram • written by Ashutosh Pandey Ashutosh Pandey

My apology. The out put file is mm9 genome WITHOUT repeats seq regions. That is all I just want to make sure.There cannot be so many repeat regions

The confusion I have is from description of such out put table at USCS site as pasted above RepeatMasker (rmsk) Track Description (http://genome.ucsc.edu/cgi-bin/hgTables ) '"In full display mode, this track displays up to ten different classes of repeats"-----

Thanks for your time and help

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updated by Ram Ram • written by kanwarjag kanwarjag

1 answer

What about BSgenome.Mmusculus.UCSC.mm9.masked?

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written by h.mon h.mon

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