TRAINING ›

Multiple Sequence Alignment and Analysis with Jalview

Venue: 
European Bioinformatics Institute, Cambridge, CB10 1SD
United Kingdom
See map: Google Maps
Date: 
Friday, November 19, 2010
Organizers: 
Geoff Barton , Dundee University
Admin support: 
Frank O'Donnell , EMBL-EBI, UK
Registration Deadline: 
Thursday, November 11, 2010
Participation: 
Open application with selection
Overview | Programme | Registration | Trainers | Speakers | Venue | Contacts

Overview

 

This course spans the basic, intermediate and advanced functions of the Jalview sequence alignment, visualisation, annotation, and analysis system. The day will begin with a lecture covering the fundamentals of sequence analysis, followed by a series of hands-on sessions where you will be able to try out different Jalview capabilities. There will also be the opportunity for participants to work with their own data, and discuss analysis problems with the Jalview team.

Is it right for me?

This course is suitable for anyone who needs to create, manipulate, annotate and publish nucleotide or protein sequence alignments, and use them to explore biological function. There will be introductory material for people with little or no experience in biological sequence analysis, but the course is also an opportunity for people with more extensive bioinformatics knowledge to gain a deeper understanding of Jalview.

Programme

 
Time Topic
Day 1 - Thursday 18th November @ Wellcome Trust, Genome Campus
19:00 - Wellcome Trust Evening Dinner
Day 2 - Friday 19th November @ EBI Training Room, Genome Campus
08:30 - 09:00 Refreshments
09:00 - 10:00 Introductory Lecture Multiple sequence alignment and analysis
10:00 - 10:40 Hands on session 1

Introduction to Jalview

  • getting started
  • loading and saving alignments
  • navigation
  • editing
  • colouring and groups
  • formatting and figure generation.
10:40 - 11:00 Refreshments
11:00 - 12:30 Hands on session 2

Alignment, annotation and analysis.

  • creating your own alignments
  • Alignment annotation
  • alignment analysis with phylogenetic trees and principal component analysis
  • working with sequence annotation
  • DNA and Protein sequences and Jalview
  • working with PDB structures
  • protein secondary structure prediction
12:30 - 13:30 Lunch
13:30 - 14:40 Hands on session 3

Advanced topics.

  1. Using Jalview to do alignments locally
    • Downloading and Installing JABA
    • Configuring Jalview for local alignment.
  2. Putting your alignments on the web with JalviewLite. 
    • Displaying an alignment in the applet on an HTML page.
    • Basic JalviewLite javascript capabilities.
14:40 - 15:00 Jalview Clinic - See what you can do with your own data in Jalview
15:00 - 15:30 Refreshments
15:30 - 15:50 Jalview clinic continues
15:50 - 16:00 Closing remarks
16:00 Departure

Registration

 

The registration fee for this workshop is £25 and includes lunches and refreshment breaks on the day as well as your meal and accommodation on the previous night. You will need to pay by credit card as you submit your registration - therefore please have your card to hand.

Registration Closed

Tags:
bioinformatics