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Introduction to Bioinformatics

Introduction to Bioinformatics. Dr. Rybarczyk, PhD University of North Carolina-Chapel Hill brybar@med.unc.edu. What is Bioinformatics?. What is Bioinformatics?.

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Introduction to Bioinformatics

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  1. Introduction to Bioinformatics Dr. Rybarczyk, PhD University of North Carolina-Chapel Hill brybar@med.unc.edu

  2. What is Bioinformatics?

  3. What is Bioinformatics? Conceptualizing biology in terms of molecules and then applying “informatics” techniques from math, computer science, and statistics to understand and organize the information associated with these molecules on a large scale

  4. Objectives: Identify appropriate search tools for your needs Perform searches using ‘unknown’ sequence data Analyze protein structure using Protein Explorer

  5. Why do we use Bioinformatics? Store/retrieve biological information (databases) Retrieve/compare gene sequences Predict function of unknown genes/proteins Search for previously known functions of a gene Compare data with other researchers Compile/distribute data for other researchers

  6. Genomic sequence RNA function & structure Protein sequence Protein structure Protein Function Phenotype Central Dogma DNA RNA Protein

  7. Computer Tools Used in Bioinformatics Sequence retrieval: NCBI GenBank Internet resources Sequence comparison programs: BLAST GCG MacVector Protein Structure: modeling prediction programs – RasMol, Protein Explorer

  8. Similarity Searching: A tool for searching gene or protein sequence databases for related genes of interest Alignments between the query sequence and any given database sequence, allowing for mismatches and gaps, indicate their degree of similarity The structure, function, and evolution of a gene may be determined by such comparisons

  9. Algorithms Computer comparisons using mathematical probabilities output input Finds best matching pair comparisons of sequences

  10. 70% MRCKTETGAR 90% MRCGTETGAR % similarity CATTATGATA GTTTATGATT

  11. Compare sequence with known sequences Translate DNA into protein sequence Understand protein function in context Sequence Analysis: Determine correct sequence of DNA

  12. Current Tools Used in Bioinformatics Strengths: Accessibility Growing rapidly User friendly Weaknesses: Sometimes not up-to-date Limited possibilities Limited comparisons and information Not accurate

  13. Need for improved Bioinformatics Genomics: Human Genome Project Gene array technology Comparative genomics Functional genomics Proteomics: Global view of protein function Protein motifs Structural databases

  14. Data Mining Handling enormous amounts of data Sort through what is important and what is not Manipulate and analyze data to find patterns and variations that correlate with biological function

  15. http://bioinformatics.weizmann.ac.il/cards/

  16. 3-D Protein Modeling • Uses information determined by crystal structure methods • Visualization of protein structure • Make protein-protein comparisons • Used to determine: conformation/folding antibody binding sites protein-protein interaction sites computer aided drug design

  17. Summary • Introduction to Bioinformatics tools: Genbank, BLAST, GCG, GeneCard, Chime How Bioinformatics is used Advantages and disadvantages of tools Applications

  18. educators students bioinformatics researchers institutions

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