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Practical Applications of Sequence Analysis

Practical Applications of Sequence Analysis. MIC 753 - The Theory and Application of Sequence Analysis. Instructor (Me). Elliot Lefkowitz Office: BBRB 277A Phone: 4-1946 E-mail: ElliotL@uab.edu. Time and Place. April 3 to June 5 2001 no class May 17 no class May 29 Tuesdays: 3:00 – 4:30

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Practical Applications of Sequence Analysis

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  1. Practical Applications of Sequence Analysis MIC 753 - The Theory and Application of Sequence Analysis

  2. Instructor (Me) • Elliot Lefkowitz • Office: BBRB 277A • Phone: 4-1946 • E-mail: ElliotL@uab.edu

  3. Time and Place • April 3 to June 5 2001 • no class May 17 • no class May 29 • Tuesdays: 3:00 – 4:30 • Thursdays: 1:00 – 2:30 • BBRB 170

  4. World-Wide-Web Site • http://genome.microbio.uab.edu/MIC753 • General Information • Handouts • Lecture Notes • Discussion List • Links

  5. Discussion List • Talk with Elliot • Ask questions • Get answers • Express your frustration • Public!

  6. Email ElliotL@uab.edu • Talk with Elliot • Ask questions • Get answers • Express your frustration • Private! • Send me your Email Address!!

  7. Sequence analysis at UAB http://genome.microbio.uab.edu • Many local sites mentioned in this course have links from this page

  8. Course Content • Tools for Sequence Analysis • GCG • NCBI • Databases • Other Web-based tools • Specialized Software • Publication • Understanding their use

  9. GCGGenetics Computer Group • The Wisconsin Package • Complete package of programs for sequence analysis • Nucleic acid and Protein databases • Supporting databases

  10. GCG Costs Program and database costs are subsidized by: • UAB Health Services Foundation • UAB AIDS Center

  11. GCG Interfaces • Command line • Text based commands • UNIX • Graphics display • SeqLab • Xwindows • Windows environment • SeqWeb • Web-based sequence analysis

  12. Other Useful Programs • Available for: • Macintosh • Windows PCs • UNIX Workstations • Web-based tools

  13. Microcomputer Sequence Analysis Packages • Macintosh and IBM

  14. Pros and Cons • Initially expensive • Databases supplied on CD-ROM • Available on-line from Genbank • Packages vary in completeness • Generally easy to use

  15. Reference Material

  16. GCG Documentation • Web-based • http://genome.microbio.uab.edu/GCG/GCG10/gcgmanual.html • Username: gcg • Password: uab • Order from GCG • http://www.gcg.com/ordering/orderdocform.html • UNIX documentation

  17. GCG Users Guide GCG Manual Version 10.1 • Basic guide to UNIX • Running GCG programs • Program descriptions • Working with data • Generating graphics

  18. GCG Program Manual • Complete Program Guide • Description • Input • Output • Parameters • Algorithms • Example

  19. SeqLab User’s Guide and Tutorial • GCG XWindows Interface • Windows-like control • menus • dialog boxes • mouse control

  20. SeqWeb Interface • http://gcg.genome.uab.edu • Flat-file version • http://gcg.genome.uab.edu:90 • Relational database version • Web-based access to GCG programs • Online help

  21. Sequence Analysis Texts

  22. A Practical Guide to the Analysis of Genes and Proteins •  Strongly Recommended • Editors • Andreas Baxevanis • B.F.Francis Ouellette • John Wiley & Sons, 1998

  23. Sequence, Structure, and Databanks : A Practical Approach • Editors • Des Higgins • Willie Taylor • Oxford Univ Press, 2000

  24. Sequence Analysis Primer • Editors • Michael Gribskov • John Devereux • Groves Press, 1991

  25. Sequence Analysis in Molecular Biology • Gunnar von Heijne, Editor • Academic Press, 1987

  26. Phylogenetic Analysis Texts

  27. Molecular Systematics • David M. Hillis and Craig Moritz (eds.) • Sinauer Associates, 1990

  28. MacClade • Analysis of Phylogeny and Character Evolution • Wayne P. Maddison and David R. Maddison • Program and Manual • Sinauer Associates, 1992

  29. PAUP 4.0 • Phylogenetic Analysis Using Parsimony • David L. Swofford • Program and Manual • Mac • PC (DOS) • UNIX • Sinauer Associates, 1998 • Available later this year

  30. Molecular Evolution • Computer Analysis of Protein and Nucleic Acid Sequences • Methods in Enzymology, Vol. 183, Doolittle, R.F. (ed.) • Academic Press, 1990

  31. Lecture Schedule

  32. http://genome.microbio.uab.edu/MIC753/schedule.htm

  33. Getting Started • Introduction; Communications • Using Computers • UNIX • Running GCG Programs • Text • Graphics • SeqLab • SeqWeb

  34. Data • Sequence and Other Data • SeqStore • Genbank Services • Sequence Editing • Fragment Assembly • Genbank submission

  35. Sequence Patterns • Mapping • Pattern Recognition • Protein Analysis

  36. Sequence Similarities • Sequence Comparison • Database Searching • Multiple Sequence Analysis • Prediction of functional motifs • Profile Analysis

  37. RNA • Secondary Structure Prediction

  38. Phylogenetic Analysis • Theory • Application

  39. MicroArray Analysis • Aubrey Hill • Director, Bioinformatics • UAB Comprehensive Cancer Center

  40. Genome Analysis • Mapping • Sequencing • Analysis

  41. Getting some real work done • Graphics and Publication • Working with your results

  42. General Lecture Outline • What the program does • What the program wants • How the program works • How can I manipulate the program? • What do I get in the end?

  43. Internet-based Tools • What is available • How do I find them? • How do I use them?

  44. Grading

  45. Class Projects • Project 1 - Preparation of Web-based Bioinformatic Solutions • Project 2 - Analysis of a gene family • Understanding • Practice A+

  46. Preparation of a Web-based Bioinformatic Solution • Each student will design a web site that describes online, web-based solutions that are available to help solve a particular bioinformatic problem. • Due Date: Monday, May 21

  47. Possible Projects • Protein motif identification • Protein structure prediction • Protein Families • RNA Secondary structure prediction • Human genome analysis • Mouse genome analysis • Microbial genome analysis • Database access and searching • Evolutionary analysis • Sequence assembly • Microarray analysis

  48. Project 1 Guidelines • You should have your topic approved by Elliot prior to beginning this project. The list below provides examples of bioinformatic problems that may be appropriate, or choose your own. • Your web site should include links to the appropriate web pages along with descriptions of what is available and a how-to guide to provide on-line help in using the bioinformatic tools. • You should also provide a review of the described sites that focuses on their ability to solve the problem at hand, and ease-of-use. • You can utilize whatever web-creation software you wish. Recommendations of easy-to-use web design programs are Microsoft FrontPage for the PC and Adobe PageMill for the Macintosh. • Up to TWO students may work on this project together and submit a common set of files for their web site.

  49. Analysis of a gene family • Each student will be required to identify a sequence family that they will analyze in different ways throughout the course. Each student must be working on a unique set of genes. Elliot will approve each choice on a first-come, first-serve basis. So it is to your advantage to accomplish the following assignment as soon as possible. • Due Date: Monday, June 11

  50. Project 2 Guidleines • Pick an interesting gene family that contains at least six members either in multiple species, or in multiple alleles. • Email a description of the gene family to Elliot (ElliotL@uab.edu) and why you think it will be worthwhile to study. • Elliot will let you know if your choice is satisfactory. If not, you will have to choose another set of genes. • Throughout the course, you should apply the various analytical programs demonstrated in class to your gene family. It will be your decision to choose which programs to use in your analysis. Your analysis should be compressive and relevant to the chosen gene family. • Prepare a short journal-type paper describing your work.

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