A one day course for anyone at Dundee University who works with biological sequences as part of their work or study. The morning session covers introductory material suitable for anyone not familiar with working with sequences and sequence alignments, or who has never edited or published alignments with Jalview. It also provides an introduction to tree based alignment analysis, which is one of the fundamental ways in which biological function and structural information can be extracted from sequence alignments.

The afternoon session provides an opportunity to explore Jalview’s web based functions, including protein secondary structure and disordered region prediction. The final session will focus on exploring 2D and 3D molecular structure information in the context of multiple sequence alignments.

The Jalview training course is a hands-on tutorial consisting of a mixture of talks and hands-on exercises. The material is based on the ‘Introduction to Jalview’ manual which is available from documentation page

Schedule for the Day

• 9am. Talk - Overview of the day.
• Session 1: 9.15am - 10.30am. Introduction to Jalview:
  • starting the application, importing alignments, basic editing and creating figures.
• Coffee: 10.30-11am.
• Session 2: 11am - 12.30pm. Alignment and alignment analysis.
  • creating sequence alignments, importing and calculating trees, tree based alignment analysis, viewing sequence annotation.
• Lunch Break. 12.30pm to 1.30pm.
• Session 3: 1.30pm - 3pm. Annotating sequences and alignments.
  • Protein secondary structure and protein disorder prediction
  • Working with alignment annotation.
• Coffee: 3pm - 3.30pm
• Session 4: 3.30pm - 4.30pm. Working with molecular structures.
  • Viewing 3D structures and superposing them using the alignment
  • Viewing RNA secondary structures.
• 4.30-4.45pm: Talk - Wrap up - what we didn’t cover today.

Date: 15-01-2013

Course: Jalview Hands On Training Course

Location Dalhousie 1G01 IT Suite 1, University of Dundee

Duration: 1 day

Posted date: 2013-05-03