IB11A

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):

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

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

* 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.

In supplementary exercises, we will investigate use of the High Performance Computing Centre (HPCC), of CPB-RAP, a national facility hosted by the Instituto Gulbenkian de Ciência. This facility offers a wide range of services including a web interface to the programs of the EMBOSS package and some applications that run faster on parallel machines.


Course Timetable
IB11A Introductory Bioinformatics, second course
Mon, December 12th
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, December 13th
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, December 14th
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, December 15th
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, December 16th
Day #5
09:30 - 11:00 High Performance Computing at the IGC
11:00 - 11:30 Coffee Break
11:30 - 12:30 Using the Staden Package for Mutations Studies
12:30 - 14:00 Lunch Break
14:00 - 16:00 Using the Staden Package for Mutations Studies
16:00 - 16:30 Tea Break
16:30 - 18:00 Practical, Wrap-up session
Course Homepage

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated:   November 8th 2011