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Up to now, there are many homology search algorithms that have been investigated and studied. However, a good classification method and a comprehensive comparison for these algorithms are absent. This is especially true for index based homology search algorithms. The paper briefly introduces main index construction methods. According to index construction methods, index based homology search algorithms are classified into three categories, i.e., length based index ones, transformation baseddoi:10.1007/s11227-006-0041-0 fatcat:hhijz2rah5a5jcbu4d6ecj3npi