Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology
String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.
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alignment problem alphabet amino acid approach binary block BLOSUM bound Boyer—Moore cell character chromosome clone column comparisons compute contains database deﬁned Deﬁnition denote diagonal discussed DNA sequence DNA string dynamic programming edge edit distance efﬁcient Euler path evolutionary exact matching example exons extension ﬁnd ﬁnding ﬁrst ﬁxed function gap weights gene genome global alignment graph Hence identiﬁed intemal node keyword tree Knuth-Morris-Pratt Knuth-Morris-Pratt algorithm labeled leaf Lemma length linear linear-time longest common matching problem matrix method mismatch molecular biology multiple alignment mutations node O(nm occurs optimal alignment overlap pair palindrome path pattem perfect phylogeny phase pointers preﬁx preprocessing proof recurrences reﬂect regular expression right end root S1 and S2 score Section shift shotgun sequencing similarity solve space speciﬁc starting at position substitution matrices substring subtree suffix sufﬁx link sufﬁx tree superstring tandem repeats Theorem traversal ultrametric ultrametric tree vector