Educators:
Alexander Goesmann, Jochen Blom, Oliver Rupp, Lukas Jelonek, Rolf Hilker (BiGi)
Date:
November 16 – November 17, 2015
Location:
Justus-Liebig-University Gießen
Room 0024a
Heinrich-Buff-Ring 58
35392 Gießen
Contents:
Topic of this two-day-workshop will be genome annotation and comparative genomics with a focus on the usage of the BIGI software tools GenDB and EDGAR. The first day will give a comprehensive introduction into microbial genome annotation. The basic principles of regional and functional annotation will be introduced, and available tools and algorithms for the different annotation steps will be explained. The GenDB genome annoation pipeline will be presented as well as a new stand-alone high-throughput annotation pipeline. Participants will get hands-on training in manual genome annotation using the GenDB web-interface. The second day will give an introduction into comparative genomics with a focus on differential gene content analysis. The use of the BLAST score ratio values (SRVs) to measure the similarity between coding sequences and to assess orthology will be introduced. The genome comparison features and genomic subset (core-genome, pan-genome, ...) calculations of the EDGAR platform for comparative genome analysis will be presented in detail. Core-genome-based phylogenetic analyses will be another topic of the second day. For hands-on training public EDGAR projects for more then 160 genera are available.
Learning goals:
Participants will be instructed in the genomics workflow and gain understanding of the possibilities and limitations of genome sequencing and sequence analysis. The course covers lectures and hands-on sessions by de.NBI experts in the fields.
Prerequisites:
The course is aimed at PhD students, postdoctoral fellows or other scientists with a solid background in bioinformatics and molecular biology.
Keywords:
Genomics, Annotation, Comparative genomics, Phylogenetic analysis, Orthology estimation
Tools:
GenDB, Prokka, Conveyor, EDGAR, BLAST, HMMER, Prodigal, PHYLIP,
Contact:
Prof. Alexander Goesmann
0641/9935800