Introduction to Bioinformatics

1. Introduction to Bioinformatics CISC 4020 Bioinformatics Spring 2013 Department of Computer and Information Science

2. Welcome to bioinformatics • This course is for • People with backgrounds in biology. • People with backgrounds in computer science. CISC 4020 Bioinformatics

3. Goal of this course • Introduction to bioinformatics • Introduction of publicly accessible databases – repositories for DNA and protein data, such as National Center for Biotechnology Information (NCBI), etc. • The analysis of DNA, RNA and proteins. • The analysis of genomes. CISC 4020 Bioinformatics

4. Outline for today • Definition of bioinformatics • Three perspectives on bioinformatics CISC 4020 Bioinformatics

5. What is bioinformatics? • The application of computer technology to organize and analyze biological data. • Analysis of proteins, genes, and genomes using computer algorithms and computer databases. • Genomics is the analysis of genomes. The tools of bioinformatics are used to make sense of the billions of base pairs of DNA that are sequenced by genomics projects. CISC 4020 Bioinformatics

6. Bioinformatics (NIH Definition) “research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, analyze, or visualize such data” CISC 4020 Bioinformatics

7. Three perspectives on bioinformatics • The cell • The organism • The tree of life CISC 4020 Bioinformatics

8. First perspective: the cell CISC 4020 Bioinformatics

9. DNA RNA protein genome transcriptome proteome Central dogma of bioinformatics and genomics Central dogma of molecular biology transcribed translated CISC 4020 Bioinformatics

10. CISC 4020 Bioinformatics

11. Focus of Bioinformatics • These millions of molecular sequences present both great opportunities and great challenges. • A main focus of bioinformatics is to study molecular sequence data to gain insight into a broad range of biological problems. CISC 4020 Bioinformatics

12. Time of development Body region, physiology, pharmacology, pathology Second perspective: the organism CISC 4020 Bioinformatics

13. Focus of Bioinformatics • The individual’s genome (collection of genes), including the genes that are expressed as RNA transcripts and the protein products are studied. • Bioinformatics tools can be applied to describe changes through developmental time, changes across body regions, and changes in a variety of physiological or pathological states. CISC 4020 Bioinformatics

14. Third perspective: the tree of life EUKARYOTE After Pace NR (1997) Science 276:734 CISC 4020 Bioinformatics

15. Tree of Life • Since all life has a common organization, it is possible to group living things according to their similar properties. • The most informative groupings reflect the relationships among both currently living and extinct organisms • shows the course of evolution that led from a single common ancestor to the present diversity of living things • This organization is known as a phylogenetic tree • The best trees are based on comparisons of DNA and protein sequences. CISC 4020 Bioinformatics

16. Focus of Bioinformatics • The scope of bioinformatics includes all of life on Earth, including three major branches of bacteria, archaea and eukaryotes. • We could further learn the variations that occur between species and among members of a species, and we can deduce the evolutionary history of life on Earth. CISC 4020 Bioinformatics