WindowMasker is a tool that identifies and masks out highly repetitive DNA sequences and DNA sequences with low complexity in a genome, using only the sequence of the genome itself. In this video, using Genome Workbench, I’ll demonstrate how to do this and at the end we’ll see the result. We start with gBench already launched. We’ll choose the open folder icon and then we’ll get Data from GenBank. We’ll choose Human Chromosome 2 with this accession NC_000002 And click ‘Next’. Choose ‘Create New Project’ and click ‘Finish.’ Now that we have the sequence we’ll open the graphical view with a right click on the sequence and then choose ‘Open View’ . Choose ‘Graphical View’ from this dialog From here we’ll go back to the ‘Search View’ tab, change the search tool to Feature Search. To this context which is the data we just retrieve and we’re going to search for the gene ‘KCMF1’ Choose the top row by selecting it here. And gBench automatically projects the selection to the graphical view, so that when we switch, we’re automatically zoomed in. Now that we have the ‘KCMF1’ gene, we’ll select it and the region around it by click and dragging in the ruler. Then right click in the ruler in the selected region and choose ‘Run Tool’. From the ‘Run Tool’ dialog, choose ‘BLAST sequences.’ Make sure the Query Sequence is selected to be the sequence with the plus, indicating the positive strand, and select the bottom sequence from the subject pane. Ensure MegaBLAST is selected from the drop down menu click ‘Next.’ From here select the WindowMasker Taxonomy ID we’d like to use. And if we need to, we can download more from NCBI. We’ll scroll down and select Homo Sapiens. Choose ‘Add to Existing Project’ – should be ‘New Project’ and click finish. It takes a few seconds for BLAST to run. Then we’ll select the alignment and choose to add a dot matrix view. In this view we see a nice straight line. Had we done this without WindowMasker, the view is quite different. I have that one save here and let’s look at it. We see a lot noise in this view along with the straight line. And that’s about it for this video. Thanks.