On a cyclic string-to-string correction problem
Information Processing Letters
Efficient parallel algorithms for string editing and related problems
SIAM Journal on Computing
SIAM Journal on Computing
Optimal surface reconstruction from planar contours
Communications of the ACM
Identifying Periodic Occurrences of a Template with Applications to Protein Structures
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
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We present a solution for the following problem. Given two sequences X = x1x2 ... xn and Y = y1y2 ...ym, n 驴 m, find the best scoring alignment of X驴 = Xk[i] vs Y over all possible pairs (k, i), for k = 1, 2, ... and 1 驴 i 驴 n, where X[i] is the cyclic permutation of X, Xk[i] is the concatenation of k complete copies of X[i] (k tandem copies), and the alignment must include all of Y and all of X驴. Our algorithm allows any alignment scoring scheme with additive gap costs and runs in time O(nm log n). We have used it to identify related tandem repeats in the C. elegans genome as part of the development of a multigenome database of tandem repeats.