Hands-on computer based workshop on retrieving sequence data from public databases, homology search tools, pairwise and multiple sequence alignments, and phylogenetic tree reconstruction.

Organizer: Lucy Skrabanek (ICB, WMC)

Goals and Objectives: This workshop is divided into four two-hour sessions. Each session begins with an introduction to the tools being taught in that session, followed by hands-on practical exercises. This workshop focuses on web-based bioinformatics tools. At the end of the workshop, attendees are expected to have a solid foundation in the use of the fundamental tools of bioinformatics.

Size: 20

Schedule:

Part 1 (day 1: 2 hours)
Students are introduced to the efficient retrieval of information and data from biological databases. We will focus mainly on the NCBI Entrez and the SRS retrieval systems.

Part 2 (day 2: 2 hours)
This section introduces homology searching tools with a particular emphasis on the BLAST suite of programs. Students learn how to optimize searches, and how to maximize biologically meaningful matches. The BLOCKS server is also described.

Part 3 (day 3: 2 hours)
Tools for pairwise and multiple sequence alignments are discussed. Students learn how best to configure the parameters in ClustalW to obtain meaningful alignments.

Part 4 (day 4: 2 hours)
The different methods of phylogenetic tree reconstruction are compared, and students are taught to evaluate the quality and robustness of the resulting tree.

Prerequisite: Experience with the web is required. Some biology background may be useful.