Dynamic FM-Index for a Collection of Texts with Application to Space-efficient Construction of the Compressed Suffix Array
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منابع مشابه
Breaking a Time-and-Space Barrier in Constructing Full-Text Indices
Suffix trees and suffix arrays are the most prominent full-text indices, and their construction algorithms are well studied. In the literature, the fastest algorithm runs in O(n) time, while it requires O(n log n)-bit working space, where n denotes the length of the text. On the other hand, the most space-efficient algorithm requires O(n)-bit working space while it runs in O(n log n) time. It w...
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The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations and applications of string indexes based on the Burrows-Wheeler transform (BWT) have been developed, all taking an amount of space that is close to the input size...
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Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search time, but it is applicable only for an alignment of similar strings without gaps. In this paper we propose the FM-index of alignment with gaps, a realistic inde...
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In this talk we address the issue of indexing compressed data both from the theoretical and the practical point of view. We start by introducing the FM-index data structure [2] that supports substring searches and occupies a space which is a function of the entropy of the indexed data. The key feature of the FM-index is that it encapsulates the indexed data (self-index) and achieves the space r...
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The collection indexing problem is defined as follows: Given a collection of highly similar strings, build a compressed index for the collection of strings, and when a pattern is given, find all occurrences of the pattern in the given strings. Since the index is compressed, we also need a separate operation which retrieves a specified substring of one of the given strings. Such a collection of ...
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تاریخ انتشار 2007