DAY 1: Thursday 18th June 2009
09.00 - 09.15
Welcome and Introduction
Miguel Andrade and Aidan Budd
09.15 - 09.45
Introduction to Teaching Machines and Common Sequence Analysis Tasks
Miguel Andrade, Aidan Budd
- Browsing the web and editing/viewing text files
- Downloading (multiple) sequences via Entrez and SRS
- Reformatting sequences (and/or alignments) using CLUSTALX
09.45 - 10.30
Introduction to Bioinformatics
Aidan Budd and Matt Huska
- common features of bioinformatic analyses and databases
- importance of measuring similarity
- accession numbers
- non-complete redundancy between many bioinformatic resources
- importance of data visualisation
10.30 - 11.00
Coffee Break
11.00 - 12.30
Sequence-Similarity Based Database Searching
Nigel Brown
12.30 - 14.00
Lunch
14.00 - 14.30
Sequence-Similarity Based Database Searching (continued)
Nigel Brown
14.30 - 18.00 (including 30 min coffee break around 15:30)
Multiple Sequence Alignment (MSA) and Phylogenies
Aidan Budd
- building an MSA and phylogeny: from A-Z
- viewing the data (alignment and tree viewers)
- sources of pre-calculated MSAs and phylogenies
20:00 – Social event – Meet at Prater Biergarten [http://www.pratergarten.de/]
Kastanienallee 7 – 9
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DAY 2: Friday 19th March 2009
09.00 – 14:30
Exploring Modular Protein Architecture (including coffee break at 10:30 and lunch break at 12:30)
Niall Haslam and Francesca Diella
- predicting globularity/non-globularity
- characterising domains
- exploring protein linear motifs
14.30 – 16:30
Exploring Protein-Protein Interactions in 3D (including a coffee break at 15:30)
Ricardo Rodriguez de la Vega
- demonstrating characteristics of domain-domain and domain-peptide interactions in 3D using PyMOL and SRS3D
16.30 - 18.00
Miguel Andrade
- threading/secondary structure prediction
18:00 – Social event – MDC Beer session
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