Working with Pathogen Genomes (Ho Chi Minh City, Vietnam)

Working with Pathogen Genomes
28 February-6 March 2010
Hospital for Tropical Diseases/Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
Deadline for applications: 30 October 2009

This five-day workshop aims to give microbiologists with a working knowledge of computational sequence analysis, a firm grounding in the use of the latest genome analysis software (Artemis and ACT) developed at the Wellcome Trust Sanger Institute Pathogen Sequencing Unit (PSU). This workshop is free to attend for non-commercial applicants and bursaries are available to cover travel and accommodation (see below for details).

Artemis is a powerful annotation tool and DNA viewer that allows the user to analyse sequence data generated in house as well as being able to upload and re-analyse data taken from databases such as EMBL or Genbank. ACT is a comparative genomic tool that allows direct, and interactive, comparisons of multiple genomes/sequences. This enables the user to exploit the growing number of genomes from closely related organisms to look at genome architecture and evolution.

The course will be taught by members of the PSU and will take the form of a series of modules covering most aspects of sequence analysis and exploitation. Each module will be introduced with a short talk followed by 'hands on' worked examples using many of the organisms sequenced by the PSU (bacterial pathogens e.g. 'Salmonella' and 'Chlamydia'), as well as small eukaryotic pathogens (such as Plasmodium and Trypanosomes) to illustrate points in whole genome analysis.

Programme

Introduction to genomics and Artemis
Overview of genome sequencing strategies and genome analysis
Understanding DNA sequence data formats
Using Artemis as a sequence analysis tool for prokaryote and small eukaryotic genomes.

De novo sequence analysis
Gene prediction and the construction of gene models
The use of other methods to support gene predictions.

Database and motif searches
Using public databases to add value to gene prediction
Principles and application of motif and domain searches
Using web based sequence analysis tools.

Sequence analysis on a larger scale
Applying search tools to large scale projects
Data interpretation
Annotation.

Comparative genomics and essential web-based genomic resources
Extensive hands on experience of the Artemis genome Comparison Tool (ACT)
Web-based information resources.

Cost
The workshop is subsidised by the Wellcome Trust and is free to attend for non-commercial applicants.The fee for commercial applicants is £1000.

Bursaries
Bursaries are available for non-commercial applicants to cover travel and accommodation costs. These are subject to a selection process and are awarded on merit. The amount awarded will depend on the number of applicants.