M. S. Waterman and M. Eggert A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Comput. Biol., 197:723-728, 1987.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....and space O(mr) In both algorithms HALF and APX LRLA, the stated objective is to compute the best possible score for a local alignment with the assumed length constraint. In general we may be interested in nding many signi cant local alignments. The algorithms proposed by Waterman and Eggert [18], and by Huang and Miller [11] nd best k non intersecting alignments for a given k . The variations of these algorithms which are based on the computations in APX LRLA can be developed so that the resulting algorithms compute approximations for the best k non intersecting alignments whose ....

M. S. Waterman and M. Eggert A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Comput. Biol., 197:723-728, 1987.

....and was also used by Goad and Kanehisa [2] Boswell and McLachlan [13] and Altschul and Erickson [14] Applications of suboptimal points will be given in the next section. The second approach to get a handle on the outrageous number of suboptimal alignments was introduced by Waterman and Eggert [15]. It is based on computing near optimal solutions to the local (Smith Waterman) alignment [6, 16] Waterman and Eggert first look for the best alternative alignment to the optimal one that does not share a residue pair with it. Subsequently, a third best alignment can be computed that intersects ....

M. S. Waterman, M. Eggert: A new algorithm for best subsequence alignments with application to trna-rrna comparisons. J Mol Biol 1987, 197:723--728.

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