1. Bioinformatics “half a year in the lab can easily save you an afternoon in front of the computer….” (unknown)

2. Genome analysis - Fall 2002 Home page: www.birc.dk/studieswww.birc.dk/studies Book: “Bioinformatics: Sequence and Genome Analysis” by D. W. Mount Teachers: Leif Schauser, Christian Storm and others Instructors: Niels Høgslund Jørgensen

4. Genome projects OrganismYearSize (Mbp)# of Genes Saccharomyces cerevisiae 1996125.200 Caenorhabditis elegans 199810019.000 Drosophila melanogaster 200011513.000 Arabidopsis thaliana 200011525.000 Human2001270039.000

5. Genomes First genomes were selected in order to reflect biological diversity. Database contains 20 10^9 bp Doubling time: 15 month –CPU doubling time 18 month Effective tools for sequence analysis needed

6. Bioinformatics Master MastersThesis Algorithms in Bioinformatics Complex systemsProtein structure Algorithms and Datastructure Molecular Population Genetics and Evolution Biostatistics Basics in Programming Mathematics basic Molecular biology basics Intro: Bioinformatics Genome analysis

7. Discuss with your neighbour What do you expect to learn during this course?

8. Topics Substitution matrices Pairwise alignment Multiple alignment RNA secondary structure prediction Phylogenetic analysis Database searching

9. Objectives Overview: understanding of topics and techniques –Motivation / principles –Mathematical and statistical models –Algorithms User-focus –When and how to use applications

10. Non-objectives To learn how to write programs To construct mathematical and statistical models To improve algorithms

11. Alignment: a central problem Alignments are basis of many analysis –Predicting RNA secondary structure –Phylogeny reconstruction –Database searches –Genome analysis mm.

12. Why alignment? Discuss with your neighbour: –Which principle does an alignment represent

13. Why alignment? Biological sequences are related –Common ancestors –Duplication, mutation, speciation, variation –Principle of evolution

14. Why alignment?

17. Ribosome structure

18. Rimosome rRNA

19. Conclusions Bioinformatic methods are motivated by the explosion of sequence data This course gives a broad introduction to a number of analysis tools Most of these tools rely on the principle of evolution

20. Schedule Lectures: Tuesdays 9-11, auditorium D1, Department of Mathematical Sciences and on Fridays 9-10, also auditorium D1 Computer / theoretical exercises take place on Wednesdays 14-17 (HOLD 1), and Thursday 11- 14 (HOLD 2) at the Department of Computer Sciences, building 540, room K.16.

22. Daimi: some practical things Unix introduction Computer exercises Username / password Sign web & user ‘brugererklaeringer’ Keys / Copy accounts

23. What is a Sequence Alignment? HIGHLY RELATED: HBA_HUMAN GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKL G+ +VK+HGKKV A+++++AH+D++ +++++LS+LH KL HBB_HUMAN GNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKL RELATED: HBA_HUMAN GSAQVKGHGKKVADALTNAVAHV---D--DMPNALSALSDLHAHKL ++ ++++H+ KV + +A ++ +L L+++H+ K LGB2_LUPLU NNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKG SPURIOUS ALIGNMENT: HBA_HUMAN GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD----LHAHKL GS+ + G + +D L ++ H+ D+ A +AL D ++AH+ F11G11.2 GSGYLVGDSLTFVDLL--VAQHTADLLAANAALLDEFPQFKAHQE How to filter out the last one & pick up the second?