IB13S

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.

* 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 (provisional)

IB13S	Introductory Bioinformatics
Mon, Dec 9th	Day #1
09:30 - 11:00	Introduction. What is Bioinformatics? Sequence databases
11:00 - 11:30	Coffee Break
11:30 - 12:30	Information Resources available through the Internet I
12:30 - 14:00	Lunch Break
14:00 - 16:00	Information Resources available through the Internet II
16:00 - 16:30	Tea Break
16:30 - 18:00	Genome Databases
Tue, Dec 10th	Day #2
09:30 - 11:00	Morning Wrap-up (what have we done so far?) Genome Databases (primarily Ensembl)
11:00 - 11:30	Coffee Break
11:30 - 12:30	Graphical Pairwise Alignments
12:30 - 14:00	Lunch Break
14:00 - 16:00	Textual Pairwise Alignments
16:00 - 16:30	Tea Break
16:30 - 18:00	Database Searching Methods (primarily blast)
Wed, dec 11th	Day #3
09:30 - 11:00	Morning Wrap-up (what have we done so far?) Primer design
11:00 - 11:30	Coffee Break
11:30 - 12:30	Simple Protein Sequence Analysis Secondary structure prediction Searching Protein Domain/Motif Databases
12:30 - 14:00	Lunch Break
14:00 - 16:00	Multiple Sequence Alignments I
16:00 - 16:30	Tea Break
16:30 - 18:00	Protein Sequence Analysis II
Thu, Dec 12th	Day #4
09:30 - 11:00	Morning Wrap-up (what have we done so far?) PSI-Blast
11:00 - 11:30	Coffee Break
11:30 - 12:30	3D protein structure databases
12:30 - 14:00	Lunch Break
14:00 - 16:00	Protein Structure Vsualization Intrinsic Protein Disorder
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: Nov 16th 2013