BackgroundIntroduction of spaced speeds opened a way of sensitivity improvement in homology search without loss of search speed. Since then, the efforts of finding optimal seed which maximizes the sensitivity have been continued today. The sensitivity of a seed is generally computed by its hit probability. However, the limitation of hit probability is that it computes the sensitivity only at a specific similarity level while homologous regions usually distributed in various similarity levels. As a result, the optimal seed found by hit probability is not actually optimal for various similarity levels. Therefore, a new measure of seed sensitivity is required to recommend seeds that are robust to various similarity levels.
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