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Bioinformatics BIO520/INF520 Jim Lund Assigned reading: Ch1 & 2

Bioinformatics BIO520/INF520 Jim Lund Assigned reading: Ch1 & 2. Bioinformatics.

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Bioinformatics BIO520/INF520 Jim Lund Assigned reading: Ch1 & 2

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  1. Bioinformatics BIO520/INF520 Jim Lund Assigned reading: Ch1 & 2

  2. Bioinformatics Bioinformatics applies principles of information science (derived from applied math, computer science, and statistics) to make the vast, diverse, and complex life sciences data more understandable and useful. It automates simple but repetitive types of analysis. Computational biology uses mathematical and computational approaches to address theoretical and experimental questions in biology.

  3. BIO520 Topics • Navigating biological databases. • Sequence alignment. • Proteins • 3D structure visualization, prediction, motif analysis. • DNA sequence annotation. • Gene finding in prokaryotes and eukaryotes. • RNA structure. • Phylogenetic inference • Genome/transcriptome/proteome • Function & Analyses.

  4. Molecular information-DNA • Raw bacterial DNA sequence • Coding or not? • Parse into genes? • Find regulatory sequences? • PCR primers, vector engineering? • 4 bases: ACGT • 1kb for a gene • Mb for a genome

  5. http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html

  6. Protein Structure Prediction

  7. MALDI-TOF? ESI-MS? Proteomics 1978-1998

  8. Metabolic Networks KEGG, 1998

  9. Regulatory Networks KEGG

  10. Acquisition, curation, and analysis of biological data Hypothesis Bioinformatics-what is it? DATA INFORMATION KNOWLEDGE

  11. DNA sequence Gene expression Protein expression Protein Structure Genome mapping Metabolic networks Regulatory networks Trait mapping Gene function analysis Scientific literature Bioinformatic Data-1978 to 2008

  12. Goals of the HGP,1998-2003 • Reference Human Genome Sequence • Draft 2001, Finished in 2003 • Improved Sequence Technology • $0.25 per finished base • Human Genome Sequence Variation • Technology for Functional Genomics • Comparative Genomics • Finish Mouse by 2005 (well ahead here) • ELSI Genome sequences highlight the finiteness of the set of sequences!

  13. What remains to be done? • Comparative Genomics • Description of mRNAs, proteins (identity and structure) • Functional analysis • Detailed understanding of development, regulation, variation

  14. The Gene for…

  15. Other Reasons to Care Affymetrix Genentech

  16. Biologist User Training • Internet sites • Range from high quality to unreliable. • Unread documentation • Popular program sites with NO documentation • Perhaps one day I will get around to writing some documentation”- • Help from a WWW service, hit several hundred times per day!

  17. Dramatic Changes in Information Science • Information Storage • Digital: text, numbers, images • Computerized Data Analysis • Automated Data Analysis • Information Distribution • Internet, cloud, etc.

  18. Moore’s Law Intel Corporation

  19. Computer Science and bioinformatics • Operating Systems • Programming • Algorithms • New problems keep turning up! • Data structure/databases • Interfaces • Search and visualization

  20. Syllabus & Schedule Textbook Internet Program documentation Labs on Fridays In Young B-35 Exams (2 + final) Grading: 12 labs: 10 pts Exams: 50 pts Final: 50 pts BIO520 Nuts and Bolts http://elegans.uky.edu/520

  21. Textbooks Required textbook: • Understanding Bioinformatics by Marketa Zvelebil and Jeremy Baum Supplemental reading (don’t buy): • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Ed. • Baxevanis and Ouellette Biology background material: • Genes IX (Lewin) • Cell Biology (Watson et al, Darnell et al) • NCBI Bookshelf (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books&itool=toolbar)

  22. http://elegans.uky.edu/520 Locally installed Programs: Cn3D, Clustal, TreeView, Chime Web based tools: Databases Software programs Computer Resources

  23. Biological Principles Evolution by natural selection DNA->RNA->Protein StructureFunction

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