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STRING DATA STRUCTURES FOR COMPUTATIONAL MOLECULAR BIOLOGY
"... The topic of the chapter is string data structures with applications in the field of computational molecular biology. Let � be a finite alphabet consisting of a set of characters (or symbols). The cardinality of the alphabet denoted by �  expresses the number of distinct characters in the alphabet ..."
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The topic of the chapter is string data structures with applications in the field of computational molecular biology. Let � be a finite alphabet consisting of a set of characters (or symbols). The cardinality of the alphabet denoted by �  expresses the number of distinct characters in the alphabet. A string or word is an ordered list
Sorting Suffixes of a Text via its Lyndon Factorization
"... Abstract. The process of sorting the suffixes of a text plays a fundamental role in Text Algorithms. They are used for instance in the constructions of the BurrowsWheeler transform and the suffix array, widely used in several fields of Computer Science. For this reason, several recent researches ha ..."
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Abstract. The process of sorting the suffixes of a text plays a fundamental role in Text Algorithms. They are used for instance in the constructions of the BurrowsWheeler transform and the suffix array, widely used in several fields of Computer Science. For this reason, several recent researches have been devoted to finding new strategies to obtain effective methods for such a sorting. In this paper we introduce a new methodology in which an important role is played by the Lyndon factorization, so that the local suffixes inside factors detected by this factorization keep their mutual order when extended to the suffixes of the whole word. This property suggests a versatile technique that easily can be adapted to different implementative scenarios.
IOS Press External Memory Algorithms for String Problems ∗
"... Abstract. In this paper we present external memory algorithms for some string problems. External memory algorithms have been developed in many research areas, as the speed gap between fast internal memory and slow external memory continues to grow. The goal of external memory algorithms is to minimi ..."
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Abstract. In this paper we present external memory algorithms for some string problems. External memory algorithms have been developed in many research areas, as the speed gap between fast internal memory and slow external memory continues to grow. The goal of external memory algorithms is to minimize the number of input/output operations between internal memory and external memory. These years the sizes of strings such as DNA sequences are rapidly increasing. However, external memory algorithms have been developed for only a few string problems. In this paper we consider five string problems and present external memory algorithms for them. They are the problems of finding the maximum suffix, string matching, period finding, Lyndon decomposition, and finding the minimum of a circular string. Every algorithm that we present here runs in a linear number of I/Os in the external memory model with one disk, and they run in an optimal number of disk I/Os in the external memory model with multiple disks.