Download FastSearch.java and ExampleMain.java files to same directory.
Open ExampleMain.java file.
According the name of your database and query to modify queryName and databaseName in ExampleMain.java.
According the score matrix and gap penalty to modify scoreName and gapScore in ExampleMain.java.
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Modify the parameters of fix_jump, seed_num, firstStepFilterSplitSize, secondStepFilterSplitSize, finalReturnSize, firstStepPara and secondStepPara.
Execute ExampleMain.java.