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Generalized enhanced suffix array construction in external memory
Algorithms for Molecular Biology, 2017 Background Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a fundamental task when the size of ...
Felipe A. Louza +3 more
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Suffix-Sorting via Shannon-Fano-Elias Codes
Algorithms, 2010 Given a sequence T = t0t1 . . . tn-1 of size n = |T|, with symbols from a fixed alphabet Σ, (|Σ| ≤ n), the suffix array provides a listing of all the suffixes of T in a lexicographic order.
Donald Adjeroh, Fei Nan
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Suffix arrays: what are they good for? [PDF]
, 2006 Recently the theoretical community has displayed a flurry of interest in suffix arrays, and compressed suffix arrays. New, asymptotically optimal algorithms for construction, search, and compression of suffix arrays have been proposed.
Simon Puglisi (19971231) +2 more
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TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases
BMC Bioinformatics, 2018 Background Protein homology search is an important, yet time-consuming, step in everything from protein annotation to metagenomics. Its application, however, has become increasingly challenging, due to the exponential growth of protein databases.
Alan Medlar, Liisa Holm
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Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. [PDF]
PLoS Computational Biology, 2017 With the rapidly increasing volume of deep sequencing data, more efficient algorithms and data structures are needed. Minimizers are a central recent paradigm that has improved various sequence analysis tasks, including hashing for faster read overlap ...
Yaron Orenstein +4 more
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CoRR, 2016 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 ...
Tomasz Marek Kowalski +3 more
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Fast mapping of short sequences with mismatches, insertions and deletions using index structures. [PDF]
PLoS Computational Biology, 2009 With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only mismatches, but also insertions and deletions.
Steve Hoffmann +7 more
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Accelerated preprocessing in task of searching substrings in a string
Advanced Engineering Research, 2019 Introduction. A rapid development of the systems such as Yandex, Google, etc., has predetermined the relevance of the task of searching substrings in a string, and approaches to its solution are actively investigated. This task is used to create database
A. V. Mazurenko, N. V. Boldyrikhin
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Computing Maximal Lyndon Substrings of a String
Algorithms, 2020 There are two reasons to have an efficient algorithm for identifying all right-maximal Lyndon substrings of a string: firstly, Bannai et al. introduced in 2015 a linear algorithm to compute all runs of a string that relies on knowing all right-maximal ...
Frantisek Franek, Michael Liut
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These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure. [PDF]
PLoS ONE, 2014 K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation.
Qingpeng Zhang +4 more
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