Introduction to Bioinformatics Spring 2008 Yana Kortsarts, Computer Science Department Bob Morris, Biology Department.
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Introduction to Bioinformatics Spring 2008 Yana Kortsarts, Computer Science Department Bob Morris, Biology Department
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.
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
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
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
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
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.)
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)
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) DNARNAProtein transcriptiontranslation
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
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
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