The Swedish Research Council has awarded Umeå University 12.5 million SEK for five years (2008-2013) for the UCMR Research School with the aim to stimulate graduate education within the UCMR research goals. The first thematic course Basic Bioinformatics sponsored by the UCMR Research School will be given May 5-May 13, 2008. For course and contact information see below or in the calendar.

 

Course                                     Basic Bioinformatics 3 hp

Homepage                                http://soul.ucmp.umu.se/MOLB05/MOLB05.html 

 

Coursedirector                         Uwe Sauer,

                                                Phone number: 090-785 6784, Fax: 090-77 80 07

                                                e-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

Department                              Umeå Centre for Molecular Pathogenesis, UCMP

 

Date                                         May, Mon. 5 - Tues. 13, 2008  (7 days)

 

Language                                  English

 

Number of participants 10

 

Layout of the course                 The course includes lectures, group discussions, computer labs and work projects. (Lectures 9h,  and discussions 5 h, practicals 21 h)

 

Knowledgetest                         All practicals must be passed, and 2 short tests (dugga)

 

Contents of the course

 

You will learn how "raw" bioinformatics data is produced, stored and manipulated. You will learn how to efficiently apply bioinformatics tools in order to answer relevant biological questions in a problem-oriented way.

In the first part of the course, problems are centered around tasks that will introduce you to various public databases available on the WWW. You will become efficient in finding and comparing DNA as well as protein sequences.

Next is an introduction to the theory of sequence alignments: the origins of scoring matrices such as PAM250 or Blossum62, dynamic algorithms, global and local alignment methods, etc.

You will then analyze unknown sequences: try to find homologous proteins in other organisms, try to find functional and structural motifs. This part of the course includes also gene mapping projects and simple phylogenetic reconstruction.

 

 

 Literature

 

1.  "Introduction to Bioinformatics" By Arthur M. Lesk, Oxford University Press, 2nd edition (May 30, 2005), ISBN: 0199277877, (pp 360, paperback SKr ~ 350:-).

2.  "Trends guide to BIOINFORMATCS", Trends Supplement 1998, Elsevier Trends Journals. Out of print but you will obtain copies. The reviews cover all aspects of BioInformatics. I strongly recommend to read it from cover to cover! (33 pages!)

3.  Additional relevant reading will be handed out during the course.