title: HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis.
abstract: Due to the size of Next-Generation Sequencing data, the computational challenge of sequence alignment has been vast. Inexact alignments can take up to 90% of total CPU time in bioinformatics pipelines. High-performance Integrated Virtual Environment (HIVE), a cloud-based environment optimized for storage and analysis of extra-large data, presents an algorithmic solution: the HIVE-hexagon DNA sequence aligner. HIVE-hexagon implements novel approaches to exploit both characteristics of sequence space and CPU, RAM and Input/Output (I/O) architecture to quickly compute accurate alignments. Key components of HIVE-hexagon include non-redundification and sorting of sequences; floating diagonals of linearized dynamic programming matrices; and consideration of cross-similarity to minimize computations.
  
  
  BACKGROUND
  https://hive.biochemistry.gwu.edu/hive/
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Rockville, Maryland, United States of America.
authors.forename: Luis
authors.initials: L
authors.lastname: Santana-Quintero
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Rockville, Maryland, United States of America; Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America.
authors.forename: Hayley
authors.initials: H
authors.lastname: Dingerdissen
authors.affiliation: National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America.
authors.forename: Jean
authors.initials: J
authors.lastname: Thierry-Mieg
authors.affiliation: Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America.
authors.forename: Raja
authors.initials: R
authors.lastname: Mazumder
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Rockville, Maryland, United States of America.
authors.forename: Vahan
authors.initials: V
authors.lastname: Simonyan
mesh_terms: D016678:Genome; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*