Microbial Genomics

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.

Our projects mainly involve microbial genomics, metagenomics and epigenomics research. 

• Toxin-antitoxin systems

  We were part of a Sinergia project dedicated to the identification and analysis of toxin-antitoxin systems (TAS) in relationship to the antibiotic resistance phenotypes. The subject has been recognized of critical importance by the World Health Organization (WHO) in its global action plan to combat antimicrobial resistance. We use Next Generation Sequencing (NGS) experiments (e.g. Tn-seq, Mut-seq, Shotgun-seq and nEMOTE-seq) to identify toxin-antitoxin genes and their targets. We also perform data mining on the ENSEMBL Bacteria database to extract candidate TAS and build a database called TASmania.

  TASmania TASer

• DNA methylations in prokaryotes

  As a secondary topic, we are interested in extracting DNA methylation information from PacBio sequencing data to compare DNA methylations in prokaryotes. We developed a tool called PACMAN to visualize graphically methylated motifs in bacterial genomes. PACMAN

• Other expertise covered as part of the core facility services
  • genome assembly
  • annotation and comparative genomics using next generation sequencing (NGS) data
  • transcriptomics analysis using NGS data
  • metagenomics
  • mutant and structure variant identification by resequencing
  • RNAseq and ChIPseq data analysis
  • proteome clustering and ortholog/paralog classification
  • pathway and gene set enrichment analysis
• Past courses & events