Dieter De Witte

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

Comparative genomics is a powerful means to gain insight into the evolutionary processes that shape the genomes of related species. As the number of sequenced genomes increases, the development of software to perform accurate cross-species analyses becomes indispensable. However, many implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements, limiting the number of genomes that can be analyzed in one run. Here, we present a software package to unveil genomic homology based on the identification of conservation of gene content and gene order (collinearity), i-ADHoRe 3.0, and its application to eukaryotic genomes. The use of efficient algorithms and support for parallel computing enable the analysis of large-scale data sets. Unlike other tools, i-ADHoRe can process the Ensembl data set, containing 49 species, in 1 h. Furthermore, the profile search is more sensitive to detect degenerate genomic homology than chaining pairwise collinearity information based on transitive homology. From ultra-conserved collinear regions between mammals and birds, by integrating coexpression information and protein–protein interactions, we identified more than 400 regions in the human genome showing significant functional coherence. The different algorithmical improvements ensure that i-ADHoRe 3.0 will remain a powerful tool to study genome evolution.

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements

Motivation: The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected. Results: We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays. Availability and implementation: BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller Contact: Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be Supplementary information: Supplementary data are available at Bioinformatics online.

Big linked data ETL benchmark on cloud commodity hardware

Linked Data storage solutions often optimize for low latency querying and quick responsiveness. Meanwhile, in the back-end, offline ETL processes take care of integrating and preparing the data. In this paper we explain a workflow and the results of a benchmark that examines which Linked Data storage solution and setup should be chosen for different dataset sizes to optimize the cost-effectiveness of the entire ETL process. The benchmark executes diversified stress tests on the storage solutions. The results include an in-depth analysis of four mature Linked Data solutions with commercial support and full SPARQL 1.1 compliance. Whereas traditional benchmarks studies generally deploy the triple stores on premises using high-end hardware, this benchmark uses publicly available cloud machine images for reproducibility and runs on commodity hardware. All stores are tested using their default configuration. In this setting Virtuoso shows the best performance in general. The other tree stores show competitive results and have disjunct areas of excellence. Finally, it is shown that each stores performance heavily depends on the structural properties of the queries, giving an indication of where vendors can focus their optimization efforts.

A Parallel, Distributed-Memory Framework for Comparative Motif Discovery

The increasing number of sequenced organisms has opened new possibilities for the computational discovery of cis-regulatory elements (‘motifs’) based on phylogenetic footprinting. Word-based, exhaustive approaches are among the best performing algorithms, however, they pose significant computational challenges as the number of candidate motifs to evaluate is very high. In this contribution, we describe a parallel, distributed-memory framework for de novo comparative motif discovery. Within this framework, two approaches for phylogenetic footprinting are implemented: an alignment-based and an alignment-free method. The framework is able to statistically evaluate the conservation of motifs in a search space containing over 160 million candidate motifs using a distributed-memory cluster with 200 CPU cores in a few hours. Software available from http://bioinformatics.intec.ugent.be/blsspeller/

Simulation of RF‐fields in a fusion device

In this paper the problem of scattering off a fusion plasma is approached from the point of view of integral equations. Using the volume equivalence principle an integral equation is derived which describes the electromagnetic fields in a plasma. The equation is discretized with MoM using conforming basis functions. This reduces the problem to solving a dense matrix equation. This can be done iteratively. Each iteration can be sped up using FFTs.