IB12A

Introductory Bioinformatics (second course)

Detailed description

The schedule of the course will be flexible and depend on the needs of the particular group. The main body of exercises will be based on an investigation of the genetic causes of the disease aniridia. This investigation will cover many aspects of bioinformatics including (roughly in order):

* the use of information and data resources available over the Internet to identify and download specific sequence data

* mainipulating the different types of sequence data available. A soft introduction to what is different with data from NGS machines.

* the investigation of various ways to compare pairs (and larger sets) of sequences.

* searching the sequence databases for entries matching a given query sequence (database searching primarily using the program BLAST)

* a range of analyses of nucleotide sequence including: restriction mapping; primer design; gene identification; DNA to protein translation

* a number of ways to investigate protein properties. In particular, predicting secondary structure, searching for membrane spanning regions and looking for motifs, domains and patterns.

* access the protein structure databases and viewing structures

Most of the analysis will be done using web resources. For some simple analyses we will use public domain software running under Windows, primarily the EMBOSS and Staden packages.


Course Timetable
IB12A Introductory Bioinformatics
Mon, Dec 10th
Day #1
09:30 - 11:00 Introduction. Types of sequence data (including NGS)

11:00 - 11:30 Coffee Break
11:30 - 12:30 What is Bioinformatics?
12:30 - 14:00 Lunch Break
14:00 - 16:00 Information Resources available through the Internet
16:00 - 16:30 Tea Break
16:30 - 18:00 Sequence Analysis Tools and Interfaces
Tue, Dec 11th
Day #2
09:30 - 11:00 Graphical Pairwise Alignments
11:00 - 11:30 Coffee Break
11:30 - 12:30 Textual Pairwise Alignments
12:30 - 14:00 Lunch Break
14:00 - 16:00 DNA sequence analysis
16:00 - 16:30 Tea Break
16:30 - 18:00 Database Searching Methods
Wed, Dec12th
Day #3
09:30 - 11:00 Gene Prediction, Primer design
11:00 - 11:30 Coffee Break
11:30 - 12:30 Dynamic Programming
12:30 - 14:00 Lunch Break
14:00 - 16:00 Multiple Sequence Alignments
16:00 - 16:30 Tea Break
16:30 - 18:00 Protein Sequence Analysis
Thu, Dec 13th
Day #4
09:30 - 11:00 Secondary Structure Prediction
11:00 - 11:30 Coffee Break
11:30 - 12:30 Patterns and Profiles
12:30 - 14:00 Lunch Break
14:00 - 16:00 Viewing 3D protein structure
16:00 - 16:30 Tea Break
16:30 - 18:00 Sequence Analysis using IGC resources
Fri, Dec 14th
Day #5
09:30 - 11:00 NGS Data Quality issues and how to get around them when possible
11:00 - 11:30 Coffee Break
11:30 - 12:30 Extra Exercises
12:30 - 14:00 Lunch Break
14:00 - 16:00 Extra Exercises
16:00 - 16:30 Tea Break
16:30 - 18:00 Final wrap-up session
Course Homepage

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated:   Feb 20th 2012