Question: mm9 repeat seq coordinates
0
gravatar for kanwarjag
3.8 years ago by
kanwarjag960
United States
kanwarjag960 wrote:

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

 

repeat sequence mm9 • 1.6k views
ADD COMMENTlink modified 3.8 years ago by h.mon26k • written 3.8 years ago by kanwarjag960

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=

ADD REPLYlink written 3.8 years ago by Ashutosh Pandey11k

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. 

ADD REPLYlink written 3.8 years ago by kanwarjag960

Hi Kanwar, I quite didnt get what you meant above. It has been a long day for me :-) Can you elaborate or rewrite the last three lines. Thanks.

ADD REPLYlink written 3.8 years ago by Ashutosh Pandey11k

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

ADD REPLYlink written 3.8 years ago by kanwarjag960
0
gravatar for h.mon
3.8 years ago by
h.mon26k
Brazil
h.mon26k wrote:

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

ADD COMMENTlink written 3.8 years ago by h.mon26k
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