Survey on index based homology search algorithms

Xianyang Jiang, Peiheng Zhang, Xinchun Liu, Stephen S.-T. Yau
2007 Journal of Supercomputing  
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 based
more » ... x ones, and their combination. Based on the classification, the characteristics of the currently popular index based homology search algorithms are compared and analyzed. At the same time, several promising and new index techniques are also discussed. As a whole, the paper provides a survey on index based homology search algorithms.
doi:10.1007/s11227-006-0041-0 fatcat:hhijz2rah5a5jcbu4d6ecj3npi