IB11
Introductory Bioinformatics (second course)Detailed descriptionThe 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 * 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.
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Course Timetable |
IB11 | Introductory Bioinformatics |
Mon, March 28th |
Day #1
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09:30 - 11:00 | Introduction |
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, March 29th |
Day #2
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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, March 30th |
Day #3
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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, March 31st |
Day #4
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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, April 1st |
Day #5
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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 Last updated: February 12th 2011 |