Repeatmasker summary table of mm9 genome?

Question

[jeannine.diesch]

Hi,

I am looking for the Repeatmasker summary table (.tbl file) of the entire mm9 genome (% of repetitive elements). Can I find this anywhere? So far I only managed to find the masked fasta file but nowhere the .tbl that is automatically generated when running Repeatmasker. Any help would be appreciated!

Thanks Jeannine

Answer 1

[Pierre Lindenbaum]

The RepeatMasker annotation tables are named chrN_rmsk (where N represents the chromosome number) and the Tandem Repeat Finder (TRF) tables are named simpleRepeat. see:

http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/simpleRepeat.txt.gz

http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/chr2_rmsk.txt.gz

....

[jeannine.diesch]

Thanks, but I already have the annotation table of mm9 from the table browser, however even if I generate a summary there are different classes coming up. I basically only need the tbl output file for the entire mm9 genome to compare it to the tbl file I got for my sequences