Results 1 to 10 of about 58,659 (213)
A suffix tree or not a suffix tree? [PDF]
Journal of Discrete Algorithms, 2014 In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question ”Is τ a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure ...
A Apostolico +17 more
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Algorithms, 2018 We consider a sliding window W over a stream of characters from some alphabet of constant size. We want to look up a pattern in the current sliding window content and obtain all positions of the matches.
Andrej Brodnik, Matevž Jekovec
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Parallel and private generalized suffix tree construction and query on genomic data [PDF]
BMC Genomic Data, 2022 Background Several technological advancements and digitization of healthcare data have provided the scientific community with a large quantity of genomic data. Such datasets facilitated a deeper understanding of several diseases and our health in general.
Md Momin Al Aziz +2 more
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A novel linear indexing method for strings under all internal nodes in a suffix tree [PDF]
Frontiers in BioinformaticsSuffix trees are fundamental data structures in stringology and have wide applications across various domains. In this work, we propose two linear-time algorithms for indexing strings under each internal node in a suffix tree while preserving the ability
Anas Al-okaily, Abdelghani Tbakhi
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Practical Compressed Suffix Trees [PDF]
Algorithms, 2013 The suffix tree is an extremely important data structure in bioinformatics. Classical implementations require much space, which renders them useless to handle large sequence collections. Recent research has obtained various compressed representations for
Gonzalo Navarro +2 more
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Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency [PDF]
The Scientific World Journal, 2012 The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps ...
Inês Soares, Ana Goios, António Amorim
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Wavelet Trees Meet Suffix Trees [PDF]
Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015 We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings.
Babenko, Maxim +3 more
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Weighted ancestors in suffix trees [PDF]
, 2014 The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a.
D.E. Willard +6 more
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PFP Compressed Suffix Trees [PDF]
, 2021 Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string S, it produces a dictionary D and a parse P of overlapping phrases such that BWT(S) can be computed from D and P in time and workspace bounded in terms of their ...
Boucher C. +6 more
openaire +2 more sources
Non-Overlapping LZ77 Factorization and LZ78 Substring Compression Queries with Suffix Trees
Algorithms, 2021 We present algorithms computing the non-overlapping Lempel–Ziv-77 factorization and the longest previous non-overlapping factor table within small space in linear or near-linear time with the help of modern suffix tree representations fitting into ...
Dominik Köppl
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