• CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • TER - Terrestrial Ecosystem Research

News

Latest publications

ConsPred - a rule-based (re-)annotation framework for prokaryotic genomes.

The rapidly growing number of available prokaryotic genome sequences requires fully automated and high-quality software solutions for their initial and re-annotation. Here we present ConsPred, a prokaryotic genome annotation framework that performs intrinsic gene predictions, homology searches, predictions of non-coding genes as well as CRISPR repeats and integrates all evidence into a consensus annotation. ConsPred achieves comprehensive, high-quality annotations based on rules and priorities, similar to decision-making in manual curation and avoids conflicting predictions. Parameters controlling the annotation process are configurable by the user. ConsPred has been used in the institutions of the authors for longer than 5 years and can easily be extended and adapted to specific needs.
The ConsPred algorithm for producing a consensus from the varying scores of multiple gene prediction programs approaches manual curation in accuracy. Its rule-based approach for choosing final predictions avoids overriding previous manual curations.Implementation and availability: ConsPred is implemented in Java, Perl, and Shell and is freely available under the Creative Commons license as a stand-alone in-house pipeline or as an Amazon Machine Image for cloud computing, see https://sourceforge.net/projects/conspred/.

Weinmaier T, Platzer A, Frank J, Hellinger HJ, Tischler P, Rattei T
2016 - Bioinformatics, in press

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.

Laffy PW, Wood-Charlson EM, Turaev D, Weynberg KD, Botté ES, van Oppen MJ, Webster NS, Rattei T
2016 - Front Microbiol, 822

Genus Candidatus Nitrosotenuis

Candidatus Nitrosotenuis is a genus of Thaumarchaeota that can be found widely distributed in soils, freshwater, hot springs, the subsurface, and activated sludge. They may be rods or spheres and may or may not have flagella. Like other known and described Thaumarchaeota, Ca. Nitrosotenuis are aerobic chemolithautotrophs that use energy gained from the oxidation of ammonia to nitrite to fix carbon via modified 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway. At this time, no pure culture of Ca. Nitrosotenuis exists, but some of the six available enrichments with members of the genus are almost pure. It remains to be  demonstrated whether the remaining bacterial contaminants provide essential compounds to Ca. Nitrosotenuis. Enrichments of Ca. Nitrosotenuis are intolerant to high salinity (>0.3%), although they are phylogenetically related to the Group I.1a Thaumarchaeota (Nitrosopumilaceae), which includes taxa that are widely distributed in the ocean.

  1.  

Herbold CW, Lebedeva E, Palatinszky M, Wagner M
2016 - In press. in Bergey’s Manual of Systematics of Archaea and Bacteria. (William B. Whitman). John Wiley & Sons, Chichester, England