D. Sanko# and J. Kruskal (eds.). Time Warps, String Edits, and Macromolecules. Addison-Wesley. 1983.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....Given two or more sequences over some fixed alphabet #, the Longest Common Subsequence problem (LCS) asks for a maximum length sequence that occurs as a subsequence in all of the given input sequences. This is considered to be a core problem of computer science with many applications, see, e.g. [5,6,14,22,24]. With the advent of computational biology, structure comparison of RNA and of protein sequences has become a central computational problem, bearing many challenging computer science questions. In this context, the Longest Arc Preserving Common Subsequence problem (LAPCS) recently has received ....

D. Sanko# and J. Kruskal (eds.). Time Warps, String Edits, and Macromolecules. Addison-Wesley. 1983.

....proteins from these amino acid sequences in a process called translation. Most biological sequences under study are either DNA or amino acid sequences. For simplicity we call the individual letters of a given sequence nucleotides. Consult Li [34] for a biological treatment on sequences, and Sanko# [46], or Eddy et al. 12] on sequence analysis techniques. Models of evolution on biological sequences fundamentally based on the assumption that evolution induces change or substitution of nucleotides in sequences in a stochastic fashion. As such we can view the evolutionary model as a distribution ....

Sankoff, D. Time Warps, String Edits, and Macromolecules. CSLI Publications, 1982.

.... gives strong theorybased support for the common intuition that Closest Substring (W[1] hard) seems to be a much harder problem than Closest String (in FPT [8] No1 Many investigations have been made of the complexity of the similar Longest Common Subsequence problem, even for k = 2 (see, e.g. [16]) tably, this could not be expressed by classical complexity measures, since both problems are NP complete as well as both do have a PTAS. Some proofs had to be omitted and are deferred to the full paper. 2 Preliminaries and Previous Work In this section, we start with a brief introduction ....

D. Sanko and J. Kruskal (eds.). Time Warps, String Edits, and Macromolecules. Addison-Wesley. 1983. Reprinted in 1999 by CSLI Publications.

....the field of sequence algorithms. This is partly for historical reasons (many sequence and alignment ideas were first worked out for the special cases of LCS) and partly because LCS often seems to capture the desired relationship between the strings of interest. This problem has many applications [6, 14, 25]. For k = 2, the longest common subsequence is a measure for the similarity of two sequences and is, thus, useful in pattern recognition [21] text compression [22] and, particularly, in molecular biology. Sequence level investigation has become essential in modern molecular biology. The digital ....

D. Sanko# and J. Kruskal (eds.). Time Warps, String Edits, and Macromolecules. Addison-Wesley, 1983.

....a cubic time and quadratic space algorithm that recovers a longest subsequence common to three strings. 4.6 Bibliographic notes Levenshtein [1966] introduced measures of distance between strings based on indels. Applications of the LCS and related problems are discussed in more detail in Sankoff and Kruskal [1983]. The string to string edit problem is described and solved in Wagner and Fisher [1974] Approximate string matching is discussed in Ukkonen [1985] Galil and Giancarlo [1988] Landau and Vishkin [1988] and Galil and Park [1990] Chin and Poon [1994] analyze some heuristics for computing an LCS. ....

Sankoff, D., and J. B. Kruskal [1983]. Time Warps, String Edits, and Macromolecules, Addison-Wesley, Reading, Mass.

....Given two or more sequences over some fixed alphabet #, the Longest Common Subsequence problem (LCS) asks for a maximum length sequence that occurs as a subsequence in all of the given input sequences. This is considered to be a core problem of computer science with many applications, see, e.g. [4, 5, 12, 18, 19]. With the advent of computational biology, structure comparison of RNA and of protein sequences has become a central computational problem, bearing many challenging computer science questions. In this context, the Longest Arc Preserving Common Subsequence problem (LAPCS) recently has received ....

D. Sanko# and J. Kruskal (eds.). Time Warps, String Edits, and Macromolecules. Addison-Wesley. 1983. Reprinted in 1999 by CSLI Publications.

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D. Sanko# and J. Kruskal (eds.). Time Warps, String Edits, and Macromolecules. Addison-Wesley. 1983.

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S. D. and J. B. Kruskal. Time warps, string edits, and macromolecules. Addison-Wesley, Reading, Mass., 1983.

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Sankoff, D. Time Warps, String Edits, and Macromolecules. CSLI Publications, 1982.

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