Bioinformatics II (6ΕΒ05)
Instructor : Pantelis Bagos
Assistant : Kontou Panagiota
Course typeElective
Semester6
TermSpring Semester
ECTS5
Teaching hours3
Laboratory hours1
Description
The PERL Programming Language (Scalar Variables, Operators, Lists, Arrays, Hashes, Control Structures, I/O, Pattern Matching and Regular Expressions), Applications in Bioinformatics (file handling, parsing, developing algorithms, BIOPERL). Algorithms in Bioinformatics: Dynamic Programming in Bioinformatics, Algorithms for Local and Global Alignment, Other Applications of Dynamic Programming. Structural Bioinformatics: Representation of Protein Structures, Protein Fold Recognition, Structure Superposition, Homology Modelling, Threading, Docking. Transformational Grammars and Applications (RNA folding, protein structure prediction). Analysis of DNA Microarrays and other types of Gene Expression Data. Analysis of Biological Networks, Study and analysis of various types of Biological Networks such as: Protein Interaction Networks, Transcriptional Regulatory Networks, Signal Switching Networks, Metabolic - Biochemical Networks, etc. Neural Networks in Bioinformatics (prediction of structural and functional characteristics of proteins).
Course objectives

After completing the course, students are expected to:

  • Be able to solve more complex problems related to genomics, biological networks and gene expression
  • Be able to program in Perl and create simple programs for sequence analysis, pattern matching and prediction.
Textbooks/Bibliography
  • Εισαγωγή στους Αλγόριθμους Βιοπληροφορικής, NEIL C. JONES, PAVEL A. PEVZNER, ΕΚΔΟΣΕΙΣ ΚΛΕΙΔΑΡΙΘΜΟΣ ΕΠΕ, 1η/2010, ΑΘΗΝΑ
  • Οδηγός της Perl, Pierce Clinton, Χ. ΓΚΙΟΥΡΔΑ & ΣΙΑ ΕΕ, 1η έκδ./2005, ΑΘΗΝΑ
Assessment method
Written examinations
Course material
http://eclass.uth.gr/eclass/courses/DIB131/