title: Alignment of high-throughput sequencing data inside in-memory databases.
abstract: In times of high-throughput DNA sequencing techniques, performance-capable analysis of DNA sequences is of high importance. Computer supported DNA analysis is still an intensive time-consuming task. In this paper we explore the potential of a new In-Memory database technology by using SAP's High Performance Analytic Appliance (HANA). We focus on read alignment as one of the first steps in DNA sequence analysis. In particular, we examined the widely used Burrows-Wheeler Aligner (BWA) and implemented stored procedures in both, HANA and the free database system MySQL, to compare execution time and memory management. To ensure that the results are comparable, MySQL has been running in memory as well, utilizing its integrated memory engine for database table creation. We implemented stored procedures, containing exact and inexact searching of DNA reads within the reference genome GRCh37. Due to technical restrictions in SAP HANA concerning recursion, the inexact matching problem could not be implemented on this platform. Hence, performance analysis between HANA and MySQL was made by comparing the execution time of the exact search procedures. Here, HANA was approximately 27 times faster than MySQL which means, that there is a high potential within the new In-Memory concepts, leading to further developments of DNA analysis procedures in the future.
authors.affiliation: Institute of Medical Biometry and Informatics, Heidelberg, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Firnkorn
authors.affiliation: Institute of Medical Biometry and Informatics, Heidelberg, Germany.
authors.forename: Petra
authors.initials: P
authors.lastname: Knaup-Gregori
authors.affiliation: Institute of Medical Biometry and Informatics, Heidelberg, Germany.
authors.forename: Justo
authors.initials: J
authors.lastname: Lorenzo Bermejo
authors.affiliation: Institute of Medical Biometry and Informatics, Heidelberg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Ganzinger
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004247:DNA