Teachers:
Henrik Lantz, Ph.D.
Jacques Dainat, Ph.D.
Lucile Soler, Ph. D.
Nima Rafati, Ph. D.
NBIS (National Bioinformatics Infrastructure Sweden) Genome Annotation Service
Click the heading of a topic to see the lecture slides or lab instructions.
Wednesday 15th
Room: E10:4308
09.00-09.45 Lecture: Understanding Annotation (Henrik Lantz)
09.45-10.00 Practical: Get started
10.00-10.15 Coffee break
10.15-10.45 Practical: assembly check
10.45-11.30 Practical: find evidence
11.30-12.00 Practical: work with gff
12.00-13.00 Lunch
13.00-13.45 Lecture : Structural annotation - the different approaches (Jacques Dainat)
13.45-14.30 Practical: Abinitio with augustus
14.30-14.45 Coffee break
14.45-17.00 Practical: Evidence based annotation - How to prepare RNAseq (short reads)
• 14.45-15.15 Prepare data
• 15.15-16.00 Guided assembly
• 16.00-16.20 Denovo assembly
• 16.20-17.00 Quality assessment
Thursday 16th
Room: E10:4308
09.00-9.15 Summary of yesterday’s exercise
09.15-10.00 Lecture: Structural annotation - Maker (Jacques Dainat)
10.00-10.15 Coffee break
10.15-12.00 Practical: Evidence based annotation - MAKER
12.00-13.00 Lunch
13.00-14.00 Practical: Abinitio training - Augustus
14.00-14.15 Coffee break
14.15-15.45 Practical: Abinitio evidence-driven annotation - MAKER
15.45-17.00 Practical: Annotation_assessment
Friday 17th
Room: E10:4308
09.00-9.15 Summary of yesterday’s exercise
09.15-10.15 Practical: Manual curation
10.15-10.30 Coffee break
10.30-11.15 Lecture: Functional annotation (Lucile Soler)
11.15-12.00 Practical: Functional annotation (part1)
12.00-13.00 Lunch
13.00-13.45 Practical: Functional annotation (part2)
13.45-14.15 Practical: Submission to DB
14.15-14.45 Lecture: Prokaryote annotation (Lucile Soler)
14.45-15.00 Coffee break
15.00-16.00 Practical: Prokaryote annotation and visualization
16.00-17.00 Wrap-up