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gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections [PDF]
Algorithms for Molecular Biology, 2020 Background The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings.
Felipe A. Louza +4 more
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GeDi: applying suffix arrays to increase the repertoire of detectable SNVs in tumour genomes [PDF]
BMC Bioinformatics, 2020 Background Current popular variant calling pipelines rely on the mapping coordinates of each input read to a reference genome in order to detect variants.
Izaak Coleman +5 more
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Compressed Spaced Suffix Arrays [PDF]
Mathematics in Computer Science, 2014 Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance.
Gagie, Travis +2 more
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Direct construction of sparse suffix arrays with Libsais [PDF]
BMC BioinformaticsBackground Pattern matching is a fundamental challenge in bioinformatics, especially in the fields of genomics, transcriptomics and proteomics. Efficient indexing structures, such as suffix arrays, are critical for searching large datasets.
Simon Van de Vyver +4 more
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Identification of consensus RNA secondary structures using suffix arrays [PDF]
BMC Bioinformatics, 2006 Background The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences.
Nguyen Truong +2 more
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Faster run-length compressed suffix arrays [PDF]
Oasics : openaccess series in informaticsWe first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $σ$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n / r) + r \log σ+ σ\right)$ bits such that later, given character $a$ and the suffix array interval for $P$, we can find ...
Brown N. K. +4 more
europepmc +5 more sources
A fast algorithm for constructing suffix arrays for DNA alphabets
Journal of King Saud University: Computer and Information Sciences, 2022 The continuous improvement of sequencing technologies has been paralleled by the development of efficient algorithms and data structures for sequencing data analysis and processing.
Zeinab Rabea +3 more
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Fast Hybrid Data Structure for a Large Alphabet K-Mers Indexing for Whole Genome Alignment
IEEE Access, 2021 The most common index data structures used by whole genome aligners (WGA) are based on suffix trees (ST), suffix arrays, and FM-indexes. These data structures show good performance results as WGA works with sequences of letters over small alphabets; for ...
Rostislav Hrivnak +2 more
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Locally Compressed Suffix Arrays [PDF]
ACM Journal of Experimental Algorithmics, 2015 We introduce a compression technique for suffix arrays. It is sensitive to the compressibility of the text and local , meaning that random portions of the suffix array can be decompressed by accessing mostly contiguous memory areas. This makes decompression very fast, especially when various contiguous cells must be
González, Rodrigo +2 more
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RECONSTRUCTING A SUFFIX ARRAY [PDF]
International Journal of Foundations of Computer Science, 2006 For certain problems (for example, computing repetitions and repeats, data compression applications) it is not necessary that the suffixes of a string represented in a suffix tree or suffix array should occur in lexicographical order (lexorder). It thus becomes of interest to study possible alternate orderings of the suffixes in these data structures,
Franěk, F., Smyth, W.F.
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