Stefan Götz

Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.

Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. Blast2GO is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use.

MOTIVATION: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds of millions of reads. Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. The systematic detection of such biases is a non-trivial task that is crucial to drive appropriate downstream analyses. RESULTS: We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses. AVAILABILITY: Qualimap is freely available from http://www.qualimap.org.

We propose a method to reuse unmodified device drivers and to improve system dependability using vir-tual machines. We run the unmodified device driver, with its original operating system, in a virtual machine. This approach enables extensive reuse of existing and unmod-ified drivers, independent of the OS or device vendor, significantly reducing the barrier to building new OS en-deavors. By allowing distinct device drivers to reside in separate virtual machines, this technique isolates faults caused by defective or malicious drivers, thus improving a system’s dependability. We show that our technique requires minimal support infrastructure and provides strong fault isolation. Our prototype’s network performance is within 3–8 % of a native Linux system. Each additional virtual machine in-creases the CPU utilization by about 0.12%. We have successfully reused a wide variety of unmodified Linux network, disk, and PCI device drivers. 1

Energy consumption is a crucial characteristic of sensor networks and their applications as sensor nodes are commonly battery-driven. Although recent research focuses strongly on energy-aware applications and operating systems, energy consumption is still a limiting factor. Once sensor nodes are deployed, it is challenging and sometimes even impossible to change batteries. As a result, erroneous lifetime prediction causes high costs and may render a sensor network, useless before its purpose is fulfilled. In this paper, we present AEON (accurate prediction of power consumption), a novel evaluation tool to quantitatively predict energy consumption of sensor nodes and whole sensor networks. Our energy model, based on measurements of node current draw and the execution of real code, enables accurate prediction of the actual energy consumption of sensor nodes. Consequently, it prevents erroneous assumptions on node and network lifetime. Moreover, our detailed energy model allows us to compare different low power and energy aware approaches in terms of energy efficiency. Thus, it enables a highly precise estimation of the overall lifetime of a sensor network.