After completing genome assembly (see previous blog post), our students have now started 4 sessions of annotation. They have chosen among 15 proposed topics, of interest either for all bacterial genomes, or specifically to this isolate from a solvent-contaminated soil. Annotation will be by pairs of students, using by default the GenDB system, which provides a first pass automatic annotation as well as access to various bioinformatics tools.
The topics chosen are:
- solvent and/or antibiotics resistance
- anaerobic respiration
- chaperones and heat shock proteins
- metal resistances
- aerobic respiration
- prophage regions
- transposons types and copy numbers
- genomic islands
- aromatic compound metabolism
- chemotaxis and flagella
- secretion systems (type II, III, IV…)
- any toxin proteins? What are they?
A sample view of the GenDB window for a random region of the P. veronii genome:
Earlier in the year we presented rapidly the theory behind different annotation resources (Blast, GO, KEGG, etc). We provide the students with a simple guide to annotation, which of course must be followed intelligently (if it were automatic, we’d automatize it, not have students do it), and 7 teachers are available to guide this annotation effort. Some of us are microbiologists, some are bioinformaticians, and some even know both fields. 😉