mm9 repeat seq coordinates

Question

[kanwarjag]

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

[Ashutosh Pandey]

Try UCSC Table Browser.

http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=444424693_csZSxNWvzHoXz6aOdEhq0eAjM8RL&clade=mammal&org=Mouse&db=mm9&hgta_group=varRep&hgta_track=knownGene&hgta_table=0&hgta_regionType=genome&hgta_outputType=primaryTable&hgta_outFileName=

[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?

[Ashutosh Pandey]

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.

[kanwarjag]

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

Answer 1

[h.mon]

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