By   November 28, 2016

Paper “Efficient Storage and Analysis of Genome Data in Databases” accepted at BTW 2017

Authors

Sebastian Dorok (Bayer Business Services GmbH, University of Magdeburg), Sebastian Breß (DFKI GmbH), Jens Teubner (TU Dortmund University), Horstfried Läpple (Bayer HealthCare AG), Gunter Saake (University of Magdeburg), Volker Markl (TU Berlin, DFKI GmbH)

Abstract

Genome-analysis enables researchers to detect mutations within genomes and deduce their consequences. Researchers need reliable analysis platforms to ensure reproducible and comprehensive analysis results. Database systems provide vital support to implement the required sustainable procedures. Nevertheless, they are not used throughout the complete genome-analysis process, because (1) database systems suffer from high storage overhead for genome data and (2) they introduce overhead during domain-specific analysis. To overcome these limitations, we integrate genome-specific compression into database systems using a specialized database schema. Thus, we can reduce the storage overhead to 30%. Moreover, we can exploit genome-data characteristics during query processing allowing us to analyze real-world data sets up to five times faster than specialized analysis tools and eight times faster than a straightforward database approach.

Supplementary Material

Source Code: cogadb-0.4.2_btw_2017_source_code.zip (mirror)