Download Algorithms on Strings, Trees and Sequences: Computer Science by Dan Gusfield PDF

By Dan Gusfield

Commonly a space of research in laptop technological know-how, string algorithms have, lately, develop into an more and more vital a part of biology, fairly genetics. This quantity is a complete examine laptop algorithms for string processing. as well as natural desktop technological know-how, Gusfield provides wide discussions on organic difficulties which are forged as string difficulties and on equipment built to resolve them. this article emphasizes the basic principles and strategies critical to today's functions. New ways to this advanced fabric simplify tools that in the past were for the expert by myself. With over four hundred routines to enhance the fabric and boost extra subject matters, the booklet is acceptable as a textual content for graduate or complicated undergraduate scholars in computing device technology, computational biology, or bio-informatics.

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Extra info for Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology

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6: A circular string p. The linear string p~ derived from it is accatggc. problem is the following. Let p be the linear string obtained from p starting at character 1 and ending at character n. Then a is a substring of circular string p if and only if a is a substring of some circular rotation of p. A digression on circular strings in DNA The above two problems are mostly exercises in using the existence of a linear-time exact matching algorithm, and we don't know any critical biological problems that they address.

Viral DNA is not always circular, but even when it is linear some virus genomes exhibit circular properties. For example, in some viral populations the linear order of the DNA in one individual will be a circular rotation of the order in another individual [450]. Nucleotide mutations, in addition to rotations, occur rapidly in viruses, and a plausible problem is to determine if the DNA of two individual viruses have mutated away from each other only by a circular rotation, rather than additional mutations.

A tandem array with a longer base). A maximal tandem array is a tandem array that cannot be extended either left or right. Given the base p, a tandem array of ^ in S can be described by two numbers (s, k), giving its starting location in S and the number of times p is repeated. 1). Suppose S has length n. Give an example to show that two maximal tandem arrays of a given base p can overlap. Now give an O(n)-time algorithm that takes S and p as input, finds every maximal tandem array of p, and outputs the pair (s, k) for each occurrence.

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