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Advanced course on algorithms for molecular biology

FDA169, 2004HT

Status Archive
School National Graduate School in Computer Science (CUGS)
Division DCS-LTH
Owner Andrzej Lingas
Homepage http://www.cs.lth.se/home/Andrzej_Lingas/bstrona.html

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Course plan

Lectures

Several basic algorithmic biological problems will be considered:
e.g., string and sequence problem, 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

This is a new course for CUGS following a similar
course given at Lund and Copenhagen universities
in the fall of 2002.

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.

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

3. Sequence multi-alignment

4. Sequence assembly I

5. Sequence assembly II

6. Physical mapping

7. Databases

8. Phylogenetic trees

9. Protein folding

10. Sorting by reversals

11. DNA computing

Organization

The lectures and possible student presentations will be given
in two, two-day series at the department of Computer Science
at Lund university.

Literature

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

Lecturers

(tentative)

Prof. Andrzej Lingas, Philip Bille,
dr. Anders Dessmark, Eva-Marta Lundell, dr. Jesper Jansson

Examiner

Prof. Andrzej Lingas, Lund University

Examination

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

Credit

4-5 p

Organized by

Lund University

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Last updated: 2012-05-03