Multiple Hypothesis Testing for Sequence Comparisons
Michael S. Waterman, Louis Gordon · 2018
In 1970, dynamic programming was first applied to the comparison of biological sequences by Needleman and Wunsch. Their method is now called a similarity method. Since their work, many extensions and modifications have been introduced. This includes distance methods, general gap functions, multiple alignment procedures, and near-optimal methods. The chapter argues that DNA sequences, but the general theory allows analysis of protein and other sequences. It provides a tentative analysis of a multiple inference procedure presented in S. F. Altschul and B. W. Erickson. They propose as a measure of sequence similarity the minimal attained significance among all runs of matches, minimizing over all possible run lengths. When more sequences began to appear in the later 1970&s;s, it became apparent that alignment of entire sequences was frequently not the major problem of interest.