Summary: Jalview (www.jalview.org) is one of the most widely used applications for visualising and analysing DNA, RNA and protein multiple sequence alignments. Available as a web based tool and desktop application, it is designed to enable anyone working with protein, RNA and DNA sequences to investigate their structure, function and evolution, and create high-quality figures for publication.
In three online workshops, Jalview’s lead developer and outreach officer will take participants through a series of hands-on exercises covering all of Jalview’s key capabilities and latest features.
Date: Wed 29th April - Fri 1st May 2020, 1pm-5pm BST.
Venue: Online - Blackboard Collaborate
Instructors: Jim Procter (U. Dundee), Suzanne Duce (U. Dundee).
Who should attend: The course is aimed at MRes/PhD students, researchers and educators with little or no previous experience with Jalview but with a basic understanding of molecular biology and biochemistry. Experienced users are welcome to join later sessions to learn about newly added capabilities.
Preparation: Online introductory materials will be sent to course participants along with joining instructions before the start of the course.
(i) Online participation requires access to a computer with voice and audio capabilities and internet access. We will be using web based video conferencing software (Blackboard Collaborate). To avoid compatibility issues, we recommend participants install Chrome for web based participation in the course, and use headphones to minimise audio problems.
(ii) Hands-on practical activities require a computer with internet access capable of running the Jalview Desktop using either Windows, OSX or Linux. Participants will be invited to share their screen with instructors during 1:1 sessions so it is important to test that your computer is able to do this with typical video conferencing software.
Session 1 on Wed 29th April from 13.00-17.00
Getting Started with Jalview.
Participants will learn about Jalview and its capabilities, how to load, edit and save sequences, create and analyse multiple alignments (using trees and PCAs), and generate figures for publication.
Session 2 on Thu 30th April from 13.00-17.00
3D structures, Protein Secondary Structure and Disorder Prediction.
Participants will learn how to use Jalview with Jmol and UCSF Chimera to view and superimpose 3D structures linked with alignments, and apply sequence and alignment based prediction methods provided by the Dundee Resource for Sequence Analysis and Structure Prediction.
Session 3 on Fri 1st May from 13.00-17.00
From Genome to Function.
Participants will learn how Jalview allows linked analysis of DNA, RNA and protein alignments, and how to import and visualise variants from VCF files in the context of protein coding regions and 3D Structures.