THREE-WAY NEEDLEMAN-WUNSCH ALGORITHM

Publisher Summary This chapter concerns specifically the algorithm of Needleman and Wunsch and its extension to a practical three-way comparison method. The use of a gap penalty weighted for the residues involved in the secondary structure of one of the proteins seems to improve the quality of alignments. The problem here, of course, is that accurate information on the secondary structure is not always available. When such information is available, however, the use of this method is recommended, as it is easily implemented in computer programs. The Needleman–Wunsch algorithm for the comparison of more than two sequences requires a large amount of computer memory. The same algorithm can be employed for the comparison of longer sequences by carrying out the matrix calculations for a limited number of cells in L. A shortcut method similar to the one described by Kruskal and Sankoff can be used. The use of a gap penalty weighted for the residues involved in the secondary structure of one of the proteins seems to improve the quality of alignments. The problem here, of course, is that accurate information on the secondary structure is not always available.