Working with Pathogen Genomes

Course summary
This residential workshop will aim to give microbiologists who have 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).

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. For more information regarding these analysis tools see Artemis: a DNA sequence viewer and annotation tool and ACT: a DNA sequence comparison viewer.

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.

Course instructors
Dr Nick Thomson (Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Hinxton, UK)

The course will include seminars by distinguished guest speakers who will present on state-of-the-art research.

Cost
The course tuition fees are subsidised by the Wellcome Trust for scientists based in academic institutions anywhere in the world. This is a residential course, without exception, and there is a registration fee of £475 towards board and lodging for academic applicants. The fee for commercial (non-academic) applicants is £1250.

Bursaries
Limited bursaries are available for academics (50 per cent of fee) and are subject to open competition.

Applications
Applicants will be required to complete an application form containing their CV together with a 300-word outline of the relevance of the course to their research. Please note that documentation supporting their application will be required from the applicant's supervisor/head of department.

Bursaries for Wellcome Trust Advanced Courses
The Wellcome Trust subsidises all courses and workshops, so there are no tuition fees. The ‘course fee' for the UK courses (held at Hinxton) covers on-site accommodation and food for the duration of the course. Bursaries are available to assist with UK course fees, but not travel costs. We are committed to building scientific capacity in developing countries and are expanding the number of courses and workshops run outside of the UK (‘overseas' courses). There is no fee for these courses and bursaries are available for travel, sustenance and accommodation. Please see below for full details.

UK Courses (held at the Wellcome Trust Genome Campus in Hinxton)
A limited number of bursaries are available for each course. These are awarded by the selection committee according to merit. The bursary usually covers 50 per cent of the course fee, though in exceptional circumstances an application for the total course fee may be considered. Where there are many bursary applications, the selection committee may issue smaller amounts. We cannot assist with travel costs. All bursary requests to attend UK courses must be accompanied by a bursary application form. This must be completed and signed by your scientific sponsor (supervisor or head of department) and include justification for the bursary. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. We will reject incomplete applications. Both the application form and sponsor's letter must be received before the application deadline. The decision of the selection committee is final.

Overseas courses (held outside the UK)
A number of bursaries are available for each overseas course. These are awarded by the selection committee according to merit. There is no course fee.The bursary will cover travel, accommodation and sustenance. The maximum award for travel (in economy/second class) will be £750. All likely travel costs must be detailed in the overseas bursary application form, which must accompany all bursary requests for courses held outside of the UK. We will notify you of the chosen hotel and sustenance award if successful. The selection committee may judge that a partial award should be granted. We will reject incomplete applications. Both the application form and sponsor's letter must be received before the application deadline.