Results 1 - 10 of 1,362
"... The suffix tree is a very important data structure in string processing, but it suffers from a huge space consumption. In large-scale applications, compressed suffix trees (CSTs) are therefore used instead. A CST consists of three (compressed) components: the suffix array, the LCP-array, and data st ..."
Abstract - Cited by 6 (0 self) - Add to MetaCart
structures for simulating navigational operations on the suffix tree. The LCP-array stores the lengths of the longest common prefixes of lexicographically adjacent suffixes, and it can be computed in linear time. In this paper, we present new LCP-array construction algorithms that are fast and very space
- BIOINFORMATICS, 2009, ADVANCE ACCESS , 2009
"... Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hashtable based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to a ..."
Abstract - Cited by 2043 (22 self) - Add to MetaCart
of individuals. Results: We implemented BWA, a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space
"... ar ..."
- In Proc. of 18th Annual European Symposium of Algorithms, Communications and Processing (ESA , 2010
"... Abstract. The Burrows–Wheeler transform is a powerful tool for data compression and has been the focus of intense research in the last decade. Little attention, however, has been paid to the inverse transform, even though it is a bottleneck in decompression. We introduce three new in-version algorit ..."
Abstract - Cited by 3 (0 self) - Add to MetaCart
Abstract. The Burrows–Wheeler transform is a powerful tool for data compression and has been the focus of intense research in the last decade. Little attention, however, has been paid to the inverse transform, even though it is a bottleneck in decompression. We introduce three new in
- In International Conference on Algorithms and Data Structures (WADS , 2011
"... ar ..."
"... Recently a number of algorithms have been developed to search files compressed with the Burrows-Wheeler Transform (BWT) without the need for full decompression first. This allows the storage require-ment of data to be reduced through the exceptionally good compression offered by BWT, while allowing ..."
Abstract - Cited by 1 (1 self) - Add to MetaCart
fast access to the information for searching by taking advantage of the sorted nature of BWT files. We pro-vide a detailed description of five of these algorithms: BWT-based Boyer-Moore (Bell et al. 2002), Binary Search (Bell et al. 2002), Suffix Arrays (Sadakane & Imai 1999), q-grams (Adjeroh et
- SIAM J. Computing , 1989
"... Abstract. A randomised approximation scheme for the permanent of a 0-1 matrix is presented. The task of estimating a permanent is reduced to that of almost uniformly generating perfect matchings in a graph; the latter is accomplished by simulating a Markov chain whose states are the matchings in the ..."
Abstract - Cited by 360 (27 self) - Add to MetaCart
matrices in some reasonable probabilistic model for 0-1 matrices of given density. For the approach sketched above to be computationally efficient, the Markov chain must be rapidly mixing: informally, it must converge in a short time to its stationary distribution. A major portion of the paper is devoted
"... The lossless Burrows-Wheeler compression algorithm has received considerable attention over recent years for both its simplicity and effectiveness. It is based on a permutation of the input sequence − the Burrows-Wheeler transformation − which groups symbols with a similar context close together. In ..."
Abstract - Add to MetaCart
describes different algorithms and improvements for these post BWT stages including a new context based approach. Results for compression rates are presented together with compression and decompression times on the Calgary corpus, the Canterbury corpus, the large Canterbury corpus and the Lukas 2D 16 bit
"... The suffix array is a data structure formed by sorting the suffixes of a string into lexicographical order. It is important for a variety of applications, perhaps most notably pattern matching, pattern discovery and block-sorting data compression. The last decade has seen intensive research toward e ..."
Abstract - Cited by 13 (3 self) - Add to MetaCart
efficient construction of suffix arrays with algorithms striving not only to be fast, but also “lightweight” (in the sense that they use small working memory). In this paper we describe a new lightweight suffix array construction algorithm. By exploiting several interesting properties of suffixes