GMX: Instruction Set Extensions for Fast, Scalable, and Efficient Genome Sequence Alignment
Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Nick Cebry, Pau Fontova-Musté, Christopher Batten, Santiago Marco‐Sola, Miquel Moretó
Abstract
Sequence alignment remains a fundamental problem in computer science with practical applications ranging from pattern matching to computational biology. The ever-increasing volumes of genomic data produced by modern DNA sequencers motivate improved software and hardware sequence alignment accelerators that scale with longer sequence lengths and high error rates without losing accuracy. Furthermore, the wide variety of use cases requiring sequence alignment demands flexible and efficient solutions that can match or even outperform expensive application-specific accelerators.
Topics & Concepts
ScalabilityComputer scienceSequence (biology)Alignment-free sequence analysisSet (abstract data type)SoftwareVariety (cybernetics)Sequence alignmentParallel computingInstruction setRangingMatching (statistics)Multiple sequence alignmentTheoretical computer scienceArtificial intelligenceProgramming languageBiologyOperating systemGeneticsMathematicsGenePeptide sequenceStatisticsTelecommunicationsGenomics and Phylogenetic StudiesAlgorithms and Data CompressionRNA and protein synthesis mechanisms