BioSEAL
Roman Kaplan, Leonid Yavits, Ran Ginosasr
Abstract
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann architectures have limited parallelism and cannot provide an efficient solution for large-scale genomic data. Approximate heuristic methods (e.g. BLAST) are commonly used. However, they are suboptimal and still compute-intensive.
Topics & Concepts
Computer scienceParallelism (grammar)Parallel computingHeuristicDynamic programmingBase (topology)Similarity (geometry)Theoretical computer scienceScale (ratio)AlgorithmMathematicsArtificial intelligenceImage (mathematics)PhysicsMathematical analysisQuantum mechanicsAlgorithms and Data CompressionGenomics and Phylogenetic StudiesAdvanced biosensing and bioanalysis techniques