Results 1 to 10 of about 1,556 (153)
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
doaj +2 more sources
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
doaj +2 more sources
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
doaj +2 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
doaj +3 more sources
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
doaj +2 more sources
On the combinatorics of suffix arrays [PDF]
Information Processing Letters, 2013 We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of Burrows-Wheeler arrays given in [1], that we apply by reducing suffix sorting to cyclic shift sorting through the use of an ...
Gregory Kucherov +2 more
exaly +5 more sources
Locally Compressed Suffix Arrays [PDF]
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
G Navarro, Hector Ferrada
exaly +2 more sources
An Elegant Algorithm for the Construction of Suffix Arrays. [PDF]
J Discrete Algorithms (Amst), 2014 The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array consists of the sorted suffixes of a string.
Rajasekaran S, Nicolae M.
europepmc +4 more sources
Compressed Spaced Suffix Arrays [PDF]
Mathematics in Computer Science, 2017 Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data structure, either a hash table or a spaced suffix array (SSA). In this paper we show how to compress SSAs relative
Giovanni Manzini +2 more
exaly +10 more sources
A quick tour on suffix arrays and compressed suffix arrays
Theoretical Computer Science, 2011 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Roberto Grossi
exaly +4 more sources