Introduction to Bioinformatics Spring 2008

1. Introduction to BioinformaticsSpring 2008 Yana Kortsarts, Computer Science Department Bob Morris, Biology Department

2. What is Bioinformatics? • Bioinformatics is a relatively new interdisciplinary field that integrates computer science, mathematics, biology, and information technology to manage, analyze, and understand biological, biochemical and biophysical information. • Bioinformatics is a computational science and the subset of larger field of Computational Biology.

3. What is Bioinformatics? • Bioinformatics is the use of computers to study biology • Bioinformatics is the science of using information to understand biology • Bioinformatics is integration of information technology (IT) and biology • Bioinformatics is the development of computational methods for studying structure, function and evolution of genes, proteins and whole genomes

4. Course Curriculum • Ethics, Computing and Genomics • Review of Molecular Biology and Biochemistry Concepts • DNA and protein structure • Gene expression (transcription and translation) • Molecular Biology Central Dogma • Biological Research on the Web • Public Biological Databases and Data Formats • Searching Biological Databases

5. Course Curriculum • Introduction to Bioinformatics Algorithms • Sequence alignments, scoring, gaps • Algorithm Design Techniques: Exhaustive Search, Dynamic Programming • The Needleman and Wunsch Algorithm • The Smith-Waterman Algorithm • Introduction to BLAST • Multiple Sequence Alignment • Phylogenetic Trees • Introduction to Python and Biopython in UNIX environment

6. Some Terminology • Cell is a primary unit of life • Cell consists of molecules, chemical reactions and a copy of the genome for that organism • All life on this planet depends on three types of molecules: DNA, RNA and proteins

7. Some Terminology • DNA • Holds information on how cell works • RNA • Acts to transfer short pieces of information to different parts of cell • Provide templates to synthesize into protein • Proteins • Form enzymes that send signals to other cells and regulate gene activity • Form body’s major components (e.g. hair, skin, etc.)

8. DNA - Deoxyribonucleic Acid • Genetic material • Consists of two long strands • Each strand is made of: • Phosphates • Sugar • Nucleotides • A (adenine) • G (guanine) • C ( cytosine) • T (thymine)

9. DNA – Double Helix Structure

10. The Central Dogma of Molecular Biology • Information has been transferred from DNA (information storage molecule) to RNA (information transfer molecule) to a specific protein (a functional, non-coding product) transcription translation DNA RNA Protein

11. More Terminology • Transcription of DNA • DNA transcribed into RNA • RNA exits as a single-strand unit and as a double-helix as well • RNA consist of A, C, G and U (uracil) • Types of RNA • Messenger RNA – mRNA • Transfer RNA – tRNA • Ribosomal RNA – rRNA

12. More Terminology • Translation of Messenger RNA (mRNA): • mRNA is translated into protein • Proteins: • linear polymers built from amino acids • The transfer of information from DNA to specific protein via RNA takes place according to the genetic code. • The RNA sequence is divided into blocks of three letters • This block is called CODON • Each codon corresponds to the specific amino acid

13. More Terminology • Four different nucleotides are used to build DNA and RNA molecules – A, G, C, T and A, G, C, U • 20 different amino acids are used in protein synthesis • Four nucleotides can be arranged in 64 different combinations of three. • There are 64 = 4*4*4 different codons • Some codons are redundant and some have special function – to terminate the translation process