Starting annotation of the P. veronii genome #biocuration

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:

gendb_pveroniiEarlier 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. 😉

annotation_guide_schema

Schema from the annotation guide provided to our students

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