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Algorithms for Molecular Biology

2006HT

Status Cancelled
School National Graduate School in Computer Science (CUGS)
Division DCS-LTH
Owner Andrzej Lingas

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Course plan

Lectures

Several basic algorithmic biological problems will be considered:
e.g., string and sequence problem, fragment assembly, protein
folding, construction of evolutionary trees etc. The final lecture
will be devoted to DNA computing.

Recommended for

students having interest in algorithms/complexity theory
or/and bioinformatics

The course was last given

A similar course for CUGS was given at university in the fall of 2004.

Goals

The purpose of the course is to give in-depth insight in the
construction and analysis of algorithms and data structures for
(primarily, molecular) biological applications.

Several biological problems which require algorithmic solutions are considered, e.g., various string and sequence problems, protein folding, construction of evolutionary trees etc. Even molecular computing, databases and internet resources accessible within molecular biology are discussed.

Prerequisites

Basic courses in algorithms and data structures, and discrete
mathematics

Contents

The tentative plan of the course is as follows.

1. Introduction
2. Sequence alignment and multiple-alignment
3. Fragment assembly
4. Physical mapping
5. Databases
6. Phylogenetic trees
7. Protein folding
8. Sorting by reversals
9. DNA computing
10. Algorithmic problems in drug design

Organization

The lectures and possible student presentations would be given
in two, two-day series at the department of Computer Science
at Lund university (September/October?)

Literature

The course is based on fragments of several textbooks (especially that
by Setubal and Meidanis on molecular computational biology) and
articles.

Lecturers

Prof. Andrzej Lingas, Eva-Marta Lundell, Mia Persson,
dr. Krzysztof Pawlowski (Astra-Zeneca)

Examiner

Prof. Andrzej Lingas, Lund University

Examination

The examination will be based on evaluation of homework assignments
and student paper presentations

Credit

5 credits

Organized by

Lund university (CUGS)

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Last updated: 2012-05-03