Algorithms for Genomes (course code: 430077)

♦ ♦ ♦ IMPORTANT ANNOUNCEMENTS ♦ ♦ ♦ RESIT EXAM RESULTS You can find the exam results here. Drop by to my office to see the exam. You can find the final grades here. CHANGE OF THE ROOM FOR THE EXAM The exam will be held on Monday, 6 Feb 06 18:30-21:30 in room Q112. FINAL GRADES You can find the final grades here. ASSIGNMENT 2 TESTS You can find the tests for the second assignment here. EXAM You can find the exam results here. You will be able to look at your exam on Tue, 10-Jan-06 13:30-14:30 (group A, with the question about Genetic code), or on Wed, 11-Jan-06, 13:30-14:30 (group B). ASSIGNMENT 2 You can find the grades for the second assignment here. ASSIGNMENT 1 You can find the grades for the first assignment here. CONSULTATIONS If you have a question about the content of the lecture I will be waiting in my office S2.56 (close to the lecture room) on Fridays, 2pm-3pm. If you have a question to another lecturer, please contact me anyway. I will answer or forward your question. TRIAL EXAM A trial exam is available (when printing, do not forget this task). You can expect the real exam to have a similar form. BIOLOGY KEYWORDS A list of biological terms you might find useful to understand. Poster is available here.

♦ General Course Info Title: Algorithms for genomes Organizer: Radek Szklarczyk (radek@cs.vu.nl) Lecturers: Nicola Armstrong, Mathisca de Gunst, Jaap Heringa, Jan Kooter, Radek Szklarczyk Teaching Assistant: Jaap Weel Audience: Bachelor and master students of Beta sciences. Tuition: The course consists of a series of lectures and one practical assignment. Course credits: 6 Grade: Based on a written exam (50%) and assignments (50%) Code: 430077 All course lectures will take place in weeks 36 - 49 on Tuesday from 13:30 to 15:15, room S2.03.

♦ Content Introduction: A gentle introduction to molecular biology and genome biology: lectures explaining principles of biology required for the course. No additional biological knowledge expected! Sequences: Sequence comparison, searching large amounts of biological data, Hidden Markov models for sequences, detecting genes and motifs. Genomes: Sequencing and assembling, genome duplication, rearrangements, evolution, comparative genomics, genome repeats Literature: Biological Sequence Analysis, R. Durbin et al.; An Introduction to Bioinformatics Algorithms, N. Jones and P. Pevzner; DNA from the Beginning

♦ Schedule Date Room Lecture Title Lecturer Lecture Slides Assignments and Resources [wk 36] 06/09/05 S2.03 Introduction to biology of the genome I Jan Kooter (email) Announced by email and available on blackboard Reading:, pp. 1-16 from Hunter, L., Molecular Biology for Computer Scientists. Artificial Intelligence for Molecular Biology, Ed. L. Hunter, AAAI Press, 1993 (pdf) [wk 37] 13/09/05 K1B74 (Trans) Introduction to biology of the genome II Jan Kooter Announced by email and available on blackboard Reading:, pp. 16-35 from Hunter, L. et al. [wk 38] 20/09/05 K1B74 (Trans) Motif discovery Nicola Armstrong Lecture 3 (handout) Additional reading have found a new home on blackboard [wk 39] 27/09/05 S2.03 Motif discovery Nicola Armstrong Lecture 4 (handout v2) Assignment 1: motifs [wk 40] 04/10/05 S2.03 Sequence comparison: Homology; Global Alignment; Radek Szklarczyk Lecture 5 (screen, handout)   [wk 41] 11/10/05 S2.03 Sequence comparison: Local alignment; Matrices; Radek Szklarczyk Lecture 6 (screen, handout) [wk 42] 18/10/05 S2.03 Sequence comparison: Alignment statistics; Searching long sequences: Blast; Blat; Blastz Radek Szklarczyk Lecture 7 (screen, handout) Reading: The Statistics of Sequence Similarity Scores Assignment 2: circular alignment [wk 44] 01/11/05 S2.03 Genome evolution and phylogeny Jaap Heringa Lecture 8 (screen, handout) [wk 45] 08/11/05 S2.03 Sequencing genomes: assembling genomic sequence; hierarchical vs shotgun method; contigs; ARACHNE program Radek Szklarczyk Lecture 9 (screen, handout)   [wk 46] 15/11/05 S2.03 Genome rearrangements: Inversional distance; permutations with/without sign; human-mouse rearrangements Radek Szklarczyk Lecture 10 (screen, handout) [wk 47] 22/11/05 S2.03 Hidden Markov Models:HMM and alignment; HMM and gene detection Mathisca de Gunst Lecture 11 (screen, handout)   [wk 48] 29/11/05 S2.03 HMM algorithms; Comparative genomics: gene detection in yeast; gene detection in mammals (TWINSCAN; SGP2) Radek Szklarczyk Lecture 12 (screen, handout)

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