Investigating the structure and function of Proteins, RNA and DNA using Jalview

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Jalview Online Introductory and Advanced Workshops: Investigating the structure and function of Proteins, RNA and DNA using Jalview

Date: Wed 29th April - Fri 1st May 2020, 1pm-5pm BST.

Venue: Online

Summary: Jalview (www.jalview.org) is one of the most widely used applications for visualising and analysing DNA, RNA and protein multiple sequence alignments. In a new online workshop format you will learn key Jalview techniques for the creation, analysis and communication of multiple sequence alignments, prediction of protein secondary structure and disorder, and visualisation of genomic variation in coding regions and mapping them onto 3D structure.

Instructors: Jim Procter (University of Dundee, UK), Suzanne Duce (University of Dundee, UK).

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.

Equipment: 

(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.

More about Jalview

Jalview is free software developed by a team managed by Geoff Barton (www.compbio.dundee.ac.uk) and Jim Procter at the University of Dundee with support from the Wellcome Trust. Jalview was recognised as an Elixir-UK Node Resource in 2016. Its interactive multi-windowed interface allows sequence alignments to be created using a range of different multiple alignment methods. Alignments can be edited, coloured and exported as figures. Three-dimensional structures and phylogenetic trees can also be linked for further analysis. Sequences and annotation can be retrieved from Ensembl, Uniprot, PDBe, Rfam and Pfam, and a range of services provide access to popular methods for calculating alignment conservation, and predicting secondary structure and protein disorder.