Bioinformatics of Virus Genomes- Course Outline

February 23 - 24, 2005
Burnaby, B.C.
CBRi Facility at BCIT-Burnaby Campus
Gait Bldg. NE25, Rm. 304
MAP

Program Leader: Dr. Chris Upton

Format of the Course

- Flexible!
- Mixture of lecture and lab time
- Often many ways to solve a given bioinformatics problem
- Choice sometimes is a personal preference
- Suggest other solutions to problems
- Provide links to other bioinformatics resources

Key Learning Objectives

1. Introduction

o Background/experience of participants

o Background/experience of presenters and project VirGO

o Why do we need specialized bioinformatics tools for analysis of virus genomes?

o Problems encountered dealing with large numbers of complete virus genomes

2. Introduction to Software Modules

o Virus Orthologous Clusters (VOCs)

o Virus Genome Organizer (VGO)

o Jdotter

o Base-By-Base (BBB)

o ReHAB

o Genome Fingerprint Scanner (GFS; mass spec searches)

3. Topics for Lecture and Lab Sessions

o Comparison of large genomes
- Differences in gene complement
- Checking genome annotation in variable sites (NAP; tBLASTn)
- Tools for displaying co-linearity of genes within genomes
(Jdotter, VGO, VOCs)

o Genome alignment
- Global alignment with Dialign2
- Viewing and correction of alignments with BBB
- Detailed summaries and graphical views with BBB

o Searching for distant homologs
- Comparison of BLASTP and PSI-BLAST
- Building families of orthologous proteins

o Motif searches in VOCs and BBB

o Use of dbEST

**Note: The course outline is subject to change. Please check the website for any updates.

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