Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust
  Database: DpseGB3    Primary Table: windowmaskerSdust    Row Count: 990,675   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom CH379058varchar(255)
chromStart 16int(10) unsigned
chromEnd 111int(10) unsigned

Sample Rows
 
binchromchromStartchromEnd
585CH37905816111
585CH379058176196
585CH379058795815
585CH379058860887
585CH37905810301047
585CH37905811661189
585CH37905812681285
585CH37905813081328
585CH37905815421567
585CH37905816771696

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

WM + SDust (windowmaskerSdust) Track Description
 

Description

This track depicts masked sequence as determined by WindowMasker. The WindowMasker tool is included in the NCBI C++ toolkit. The source code for the entire toolkit is available from the NCBI FTP site.

Methods

To create this track, WindowMasker was run with the following parameters: 

windowmasker -mk_counts true -input DpseGB3.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input DpseGB3.fa -output repeats.bed
The repeats.bed (BED3) file was loaded into the "windowmaskerSdust" table for this track.

References

Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941