Software and Databases

The Effective database contains pre-calculated predictions of bacterial secreted proteins and of functional secretion systems.

The "GEnome PAir - Rapid Dotter" allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes.

GenSkew is an application for computing and plotting nucleotide skew data.

NVT is an R package for the assessment of RNA-Seq normalization methods.

VOGDB, a continously updated resource of Virus Orthologous Groups (VOG) - including virus specific marker groups for metagenomics and universal groups for diversity estimation in virus ecology. Funding by: FWF grant number I1303 and MSCA Innovative Training Networks grant agreement no. 955974 (VIROINF).

HoloVir is a robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes.​​

The database PhenDB contains and provides PICA models for phenotypic trait prediction in microbial genome drafts.

Phenotrex is a component of the PhenDB web server, which performs phenotypic trait prediction on user-uploaded metagenomic bins.

The accessibility of almost complete genome sequences of uncultivable microbial species from metagenomes necessitates computational methods predicting microbial phenotypes solely based on genomic data. Comparative genomics can be utilized for the prediction of microbial phenotypes. The PICA framework facilitates application and comparison of different machine learning techniques for phenotypic trait prediction. We have improved and extended PICA's support vector machine plug-in and suggest its applicability to large-scale genome databases and incomplete genome sequences.

The similarity matrix of proteins is a database of protein sequences, their all-against-all sequence similarities and functional annotations.