Code EB3
Type Elective
Semester B
ECTS credits 4
Teaching Staff Assistant professor Christos Makris Department of Computer Engineering and Informatics, University of Patras


The topic of the course is to introduce students to the basic notions of Bioinformatics.Bioinformatics is a combination of Computer Science and Molecular Biologyfocusing atthe design of data structures and computational methods to facilitate the efficientstorage, retrieval and manipulation of biological molecules (DNA, RNA, genes, proteins).Understanding basic computational methods such as string and machine learningalgorithms and how they are used to develop software tools to process efficientlybiological data is a main objective of this course.


  • Course introduction to its main notions (Computer Science and Molecular Biology)
  • Exact string matching algorithms (Boyer – Moore, Knooth-Morris-Pratt, Aho-Corasick Automaton)
  • Suffix Trees and applications in Bioinformatics
  • Inexact matching an sequence alignment
  • Multiple sequence alignments
  • Bioinformatics Databases and Data Mining

PRACTICALS (optional)

Two projects, one a set of exercises on string algorithmics, the second a set of researchassignments where each student beginning with an initial set of papers will investigate aresearch topic.


Understanding the basic notions of Bioinformatics, understanding string algorithms andmachine learning algorithms and how they apply to problems in Computational MolecularBiology, understanding Biological databases.


Oral examination on the topic of the two projects (the set of exercises on stringalgorithmics and the research assignments) and questions about the course, Examduration: 1h. Concerning the topic of the course mainly the understanding of conceptswill be tested. The relative importance of the technical and mathematical derivations willbe pointed out during the lectures.


Understanding of basic notions of computer science and molecular biology is imperative.


  1. “Βιοπληροφορική, Δυνατότητες και Προοπτικές”, Σοφία Κοσσίδα, 2008
  2. An introduction to bioinformatics algorithms C. Jones, PavelPevzner, Cambridge,MIT 2004.
  3. Handbook of Computational Molecular Biology, edited by Srinivas Aluru, 2006,Taylor and Francis Group.
  4. Algorithms on Strings, Trees and Sequences, D. Gusfield, Cambridge UniversityPress, 1999