Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis with Jalview

Craik-Marshall Building, Downing, Cambridge. May 11-13th 2015

Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA.

Day 3 - Jpred4 - Protein Secondary Structure Prediction

• Join-Me Link to view demonstrations
• Slides and data for Day 3
• 2 minutes on M-Coffee

• Jalview 2.8.2 Manual (Screen version)
• Launch jalview with 15 GB

Day 1: Jalview Bootcamp - Introduction

• Day 1 Slides as a PDF
• Geoff Barton's Lecture on Multiple Sequence Alignment

Day 2: Structures and annotation and Jalview Clinic

• Day 2 Morning Slides (excluding quiz slides) as a PDF
• Geoff Barton's Protein Structure: A quick reminder
• Day 2 Afternoon slides
• Launch Jalview 2.9 Alpha (for cDNA/Protein, new RNA shading, and new PDBe query interface)
  Supplementary Exercises for Jalview 2.9 Alpha
• RF0031 Folded RNA example for per-sequence secondary structure display

Original description of the three day course

Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication.

The course involves of a mixture of talks and hands-on exercises.

Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview.

Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch.

Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues.

There will be opportunities for attendees to get advice on analysis of their own sequence families.

Target audience:

• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Further details regarding eligibility criteria are available here
• Further details regarding the charging policy are available here

Session: