SaAlign: Multiple DNA/RNA sequence alignment and phylogenetic tree construction tool for ultra-large datasets and ultra-long sequences based on suffix array [PDF]
Computational and Structural Biotechnology Journal, 2022 Multiple DNA/RNA sequence alignment is an important fundamental tool in bioinformatics, especially for phylogenetic tree construction. With DNA-sequencing improvements, the amount of bioinformatics data is constantly increasing, and various tools need to
Ziyuan Wang +7 more
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GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array. [PDF]
PLoS ONE, 2014 DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity.
Shuji Suzuki +3 more
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Generalized enhanced suffix array construction in external memory [PDF]
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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TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases [PDF]
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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Fast, parallel, and cache-friendly suffix array construction [PDF]
Algorithms for Molecular BiologyPurpose String indexes such as the suffix array (sa) and the closely related longest common prefix (lcp) array are fundamental objects in bioinformatics and have a wide variety of applications.
Jamshed Khan +4 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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RNA-Seq mapping and detection of gene fusions with a suffix array algorithm. [PDF]
PLoS Computational Biology, 2012 High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes.
Onur Sakarya +23 more
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A bioinformatician's guide to the forefront of suffix array construction algorithms [PDF]
Briefings in Bioinformatics, 2014 Paul Horton +2 more
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Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets [PDF]
BMC BioinformaticsIdentification of microorganisms in a biological sample is a crucial step in diagnostics, pathogen screening, biomedical research, evolutionary studies, agriculture, and biological threat assessment.
Burak Demiralay, Tolga Can
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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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