Entropy estimation with suffix arrays
نویسندگان
چکیده
منابع مشابه
Replacing suffix trees with enhanced suffix arrays
The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every algorithm that uses a suffix tree as data structure can systematically be replaced with an algorit...
متن کاملReplacing suffix trees with enhanced suffix arrays
The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every algorithm that uses a suffix tree as data structure can systematically be replaced with an algorit...
متن کاملSuffix Trees and Suffix Arrays
Iowa State University 1.1 Basic Definitions and Properties . . . . . . . . . . . . . . . . . . . . 1-1 1.2 Linear Time Construction Algorithms . . . . . . . . . . . . . 1-4 Suffix Trees vs. Suffix Arrays • Linear Time Construction of Suffix Trees • Linear Time Construction of Suffix Arrays • Space Issues 1.3 Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...
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The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show that (i) how we search for the right interval boundary impacts significantly the overall search speed, (ii) a B-tree data layout easily wins over the standar...
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ژورنال
عنوان ژورنال: Progress in Informatics
سال: 2012
ISSN: 1349-8614,1349-8606
DOI: 10.2201/niipi.2012.9.4