Introduction to Bioinformatics Algorithms: What is a bioinformatics algorithm? Representation of biological data as sequences. Basic algorithmic concepts: complexity, efficiency, correctness.
Algorithm Categories: Exhaustive (Brute-force), Greedy, Divide and Conquer.
Gene Prediction: Models such as Neural Networks, ORF detection. Training and evaluation of models. Comparison of prediction algorithms.
Recognition of Transcription Factor Binding Motifs: Motif representation, Position Weight Matrices (PWMs), consensus sequences. Motif finding algorithms: Exhaustive search, Expectation Maximization. Scanning genomic regions with motif scoring.
DNA Mapping via Partial Digestion
Transpositions and Genome Rearrangements: Genome assembly (genome rearrangement problem).
Programming Implementation and Case Study: Implementation of motif discovery, design of a simple gene predictor.
Textbooks/Bibliography
ΕΙΣΑΓΩΓΗ ΣΤΟΥΣ ΑΛΓΟΡΙΘΜΟΥΣ ΒΙΟΠΛΗΡΟΦΟΡΙΚΗΣ, NEIL C. JONES, PAVEL A. PEVZNER, ΕΚΔΟΣΕΙΣ ΚΛΕΙΔΑΡΙΘΜΟΣ ΕΠΕ, 1η/2010, ΑΘΗΝΑ
