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MOTIVATION Building the histogram of occurrences of every k-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of k-mer counting. Its applications include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. The tremendous amounts of NGS data(More)
Concurrent computing can be applied to heuristic methods for combinatorial optimization to shorten computation time, or equivalently , to improve the solution when time is fixed. This paper presents several communication schemes for parallel simulated annealing, focus-ing on a combination of OpenMP nested in MPI. Strikingly, even though many publications(More)
The k-mer counting problem, which is to build the histogram of occurrences of every k-symbol long substring in a given text, is important for many bioinformatics applications. They include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. We propose a simple, yet efficient, parallel disk-based algorithm for(More)
Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment algorithms. The article introduces FAMSA, a new progressive algorithm designed for fast and accurate(More)
The paper focuses on a parallel implementation of a simulated annealing algorithm. In order to take advantage of the properties of modern clustered SMP architectures a hybrid method using a combination of OpenMP nested in MPI is advocated. The development of the reference implementation is proposed. Furthermore, a few load balancing strategies are(More)