## 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 here.

## Methods

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

    windowmasker -mk_counts true -input $db.fa -output wm_counts
    windowmasker -ustat wm_counts -sdust true -input $db.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.