Schema for WM + SDust - Genomic Intervals Masked by WindowMasker + SDust
  Database: canFam3    Primary Table: windowmaskerSdust    Row Count: 13,644,959   Data last updated: 2012-01-06
Format description: Browser extensible data
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 100int(10) unsigned Start position in chromosome
chromEnd 1004int(10) unsigned End position in chromosome
name chr1.1varchar(255) Name of item

Sample Rows
 
binchromchromStartchromEndname
585chr11001004chr1.1
585chr110272479chr1.2
585chr125022714chr1.3
585chr127265271chr1.4
585chr152765476chr1.5
585chr154946189chr1.6
585chr161926239chr1.7
585chr162786666chr1.8
585chr166917498chr1.9
585chr175127815chr1.10

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 canFam3.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input canFam3.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