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Core/Elective: Elective Semester: 2 Credits: 3

Course Description

Present fundamental concepts from molecular biology, computational problems in molecular biology and some efficient algorithms that have been proposed to solve them.

Course Objectives

To familiarize computational problems in biology
To understand models of DNA and DNA mapping
To study structure prediction

Course Content

1. Basic concepts of molecular Biology-Proteins-Nucleic acids– genes and genetic synthesis –translation- transcription- protein Synthesis- Chromosomes- Maps and sequences- human genome project- sequence data bases

2. Strings-Graphs-Algorithms- Comparing 2 sequences- Global & Local comparison-General Gap Penalty Function-Affix gap penalty function-comparing multiple sequences-Star alignments-Tree alignments-Database Search-PAM matrices BLAST-FAST –Issues

3. Fragment Assembly of DNA-Biological Background –Models-Algorithms-Heuristics-Physical Mapping of DNA-Restriction site Mapping-site models-Internal Graph Models –Hybridization Mapping-Heuristics

4. Phylogenic Trees –Binary Character States-Parsimony and Compatibility in Phylogenies-Algorithm for Distance Matrices-Additive Trees- Genome rearrangements-Oriented Blocks-unoriented Blocks

5. Molecular Structure Prediction- RNA secondary structure prediction-Protein Folding problems-Protein threading-Computing with DNA-Hamilton Path Problems. –Satisfiability


1. Computational Molecular Biology-An introduction (1st Ed): Peter Clote and Rolf Backofen, Wiley Series (2000)
2. An introduction to Bioinformatics Algorithms (1st Ed): Neil James and Pavel A Pevzner, MIT Press (2004)

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