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   Articles with "fast memory" as a keyword



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ecmtool: fast and memory-efficient enumeration of elementary conversion modes

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recommendations! Published in 2023 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btad095

Abstract: Abstract Motivation Characterizing all steady-state flux distributions in metabolic models remains limited to small models due to the explosion of possibilities. Often it is sufficient to look only at all possible overall conversions a cell… read more here.

Keywords: ecmtool fast; conversion modes; enumeration; elementary conversion ... See more keywords
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Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btad151

Abstract: Abstract Motivation Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware acceleration. A promising candidate for all of the above is the… read more here.

Keywords: scrooge; genasm; sequence; scrooge fast ... See more keywords
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A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment

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recommendations! Published in 2020 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btz725

Abstract: MOTIVATION Multiple Longest Common Subsequence (MLCS) problem is searching all longest common subsequences of multiple character sequences. It appears in many fields such as data mining, DNA alignment, bioinformatics, text editing and so on. With… read more here.

Keywords: character merging; dna sequences; character; fast memory ... See more keywords
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SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier

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recommendations! Published in 2019 at "GigaScience"

DOI: 10.1093/gigascience/giz118

Abstract: Abstract Background Gene homology type classification is required for many types of genome analyses, including comparative genomics, phylogenetics, and protein function annotation. Consequently, a large variety of tools have been developed to perform homology classification… read more here.

Keywords: efficient multiple; swiftortho fast; fast memory; orthology ... See more keywords
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STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale

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recommendations! Published in 2022 at "Frontiers in Neuroinformatics"

DOI: 10.3389/fninf.2022.883742

Abstract: Recent advances in computational neuroscience have demonstrated the usefulness and importance of stochastic, spatial reaction-diffusion simulations. However, ever increasing model complexity renders traditional serial solvers, as well as naive parallel implementations, inadequate. This paper introduces… read more here.

Keywords: steps fast; reaction diffusion; memory; fast memory ... See more keywords