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Given a pattern string P of length n consisting of δ distinct characters and a query string T of length m, where the characters of P and T are drawn from an alphabet Σ of size ∆, the exact string matching problem consists of finding all occurrences of P in T. For this problem, we present a randomized heuristic that in O(nδ) time preprocesses P to identify… (More)

Given a pattern string P of length n and a query string T of length m, where the characters of P and T are drawn from an alphabet of size ∆, the exact string matching problem consists of finding all occurrences of P in T. For this problem, we present algorithms that in O(n∆ 2) time preprocess P to essentially identify sparse(P), a rarely occurring substring… (More)

For the static list update problem, given an ordered list ρ 0 (an ordering of the list) of requests for items in L, we characterize the list reorganizations in an optimal offline solution in terms of an initial permutation of the list followed by a sequence of m element transfers, where an element transfer is a type of list reorganization where only the… (More)

Advances in biotechnology have made available massive amounts of functional, structural and genomic data for many biological sequences. This increased availability of heterogeneous biological data has resulted in biological applications where a multiple sequence alignment (msa) is required for aligning similar features, where a feature is described in… (More)

In generalized tree alignment problem, we are given a set S of k biologically related sequences and we are interested in a minimum cost evolutionary tree for S. In many instances of this problem partial topology of the phylogenetic tree for S is known. In such instances, we would like to make use of this knowledge to restrict the tree topologies that we… (More)

In this paper, we present new approximation results for the offline problem of single machine scheduling with sequence-independent setups and item availability, where the jobs to be scheduled are independent (i.e., have no precedence constraints) and have a common release time. We present polynomial-time approximation algorithms for two versions of this… (More)

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