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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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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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 Anish M S Shrestha +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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