What do we do?
At the Bioinformatics Unraveling Group of the University of Fribourg (BUGFri), we support life science researchers by providing expertise in data analysis of Next Generation Sequencing (NGS) experiments, or any large-scale biological experiment requiring bioinformatics resources. We focus on genome assembly, annotation and comparison as well as on mutant and structure variant identification by resequencing. We also perform metagenomics, RNAseq and ChIPseq data analysis, proteome clustering and ortholog/paralog classification, as well as pathway and gene set enrichment analysis.
Highlights 2016At the beginning of 2016, the Sinergia project "Pangenomic and comprehensive analysis of the relationship between bacterial toxin-antitoxin systems and antibiotic phenotype" began. We are now working towards improving the analysis and description of toxin-antitoxin systems (TAs) using both NGS data analysis to identify cut sites of some toxins and public Tn-Seq data to identify new TAs.
The web server PACMAN (PACific biosciences Methylation Analyzer) was also improved. This web site allows a user to upload a full, or draft, bacterial genome together with the motifs.gff file of a PacBio sequencing analysis.
The PACMAN web server uses Circos to generate a graphical view of the most important methylation motifs. The user can preselect by making a choice among several possible views and filters. The output is a publication-ready PDF or PNG. In addition, the detailed page can be used to identify genes near hyper- and hypo- methylated regions. PACMAN is hosted by Vital-IT.
Main publications 2016
- Ardissone S et al. (2016). Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria. PLoS Genet 12: e1006499 (online doi:10.1371/journal.pgen.1006499).
- Leake SL et al. (2016). The salivary microbiome for differentiating individuals: proof of principle. Microbes and Infection 18: 399-405.
- Ritpitakphong U et al. (2016). The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytologist 210: 1033-1043.