1-Month Practical Master Course Integrative Bioinformatics & Genomics

♦ ♦ ♦ IMPORTANT ANNOUNCEMENTS ♦ ♦ ♦ <none>

♦ General Course Info Students who wish to follow the alternative track "Integrative Bioinformatics and Genomics" at the IBIVU, will find below the schedule of the work they are supposed to do. You will sit an oral exam on the last day of the course. Your final mark will be the (weighted) average of your written reports and your oral exam mark. The Genome Analysis course is divided in four parts. Included is a disease genome mining project, where you can choose between diabetes and malaria. All lectures will be held in P1.28.

♦ ♦ ♦ Course Schedule ♦ ♦ ♦ INDUCTION PROJECT: Do the following four assignments in full and write a detailed but succinct report for each assignment as indicated. assignment 0: Sequence Retrieval System Email your report on the assignment 0 questions to Bernd Brandt (bwbrandt@few.vu.nl - Rm P1.52) Deadline: Friday 12/09/2008 at 23:59 assignment 1: NCBI and anthrax assignment 2: BLAST and ATPase assignment 3: NCBI & Ensembl! Email your report on the assignment 1 - 3 questions to Walter Pirovano (pirovano@few.vu.nl - Rm P1.38) Deadline: Friday 12/09/2008 at 23:59 NB: wait with carrying out assignment 2 (BLAST) until after the BLAST lecture (on Tuesday 09/09/2008) If you have questions, etc., on the above four assignments (0 - 3), please consult the practical supervisor indicated. ALIGNMENT and DATABASE HOMOLOGY SEARCHING: assignment 4: Multiple Sequence Alignment assignment 5: Sequence Database Searching (or Homology Searching) Mailto: pirovano@few.vu.nl Deadline: Tuesday 23/09/2008 at 23:59 (assignment 4 & 5) DISEASE GENE MINING MINI-PROJECT and WRITING REPORT: Carry out a mining project + write final report Genome mining (Insulin or Malaria): Read background on Diabetes or Malaria depending on topic selected (disease magnitude, molecular and disease principles, life cycle (malaria), host-parasite relationships (malaria), etc.) and homology modeling. Write report containing most important conclusions as introduction to final report. Links to relevant information: Malaria: http://www.wehi.edu.au/MalDB-www/intro.html and http://www.tigr.org/tdb/edb2/pfa1/htmls/index.shtml Insulin: http://www.endocrineweb.com/diabetes/2insulin.html and http://en.wikipedia.org/wiki/Insulin Insulin stucture: http://www.vivo.colostate.edu/hbooks/pat\ hphys/endocrine/pancreas/insulin_struct.html Genbank: http://www.ncbi.nlm.nih.gov/Genbank/ SWISSPROT/UNIPROT and trEMBL database: http://www.expasy.org/sprot/ Silkworm database: http://silkworm.genomics.org.cn For the Kleinjung et al. paper about IGF mining in the Drosophila genome, click here. Note: the part on Drosophila mining is in the back of this article. GENOME MINING TASK: Each student mines a genome where one of the following options can be selected: Malaria: Select one of various malaria genomes; mollucs, bombyxin Diabetis: Select one of various fly genomes for insulin-like (receptor) genes). Mining includes finding genes and putative gene functions. Tools to use are (PSI-)BLAST; multiple alignment with PRALINE, T-COFFEE, MUSCLE, or PROBSCONS; Sequence Harmony, and phylogeny methods (e.g. Neighbour Joining -- can be found on the web). Note: check the IBIVU programs page to find some of the software you need. Mine a genome (or the BLAST non-redundant (NR) database) with disease gene(s) of choice, for example, try to predict the function of the SARS gene set (particularly the missing gene functions). WRITING REPORT: Write final report and email it to pirovano@few.vu.nl EXAM PREPARATION Send an email to heringa@few.vu.nl to make an appointment for the oral exam. Make sure you have completed your mining assignment and have submitted your report before you sit your exam.

♦ ♦ ♦ Lecture Schedule ♦ ♦ ♦ The schedule below is a preliminary schedule! Dates, times and subjects might swap or change. ♦ Date Time Lecture Title View Slides Other resources Tue 02/09/2008 10:00-12:00 Lecture 1: Introduction PowerPoint or PDF or PDF_handout format Information on Genes and Genomes in PowerPoint or PDF format Wed 03/09/2008 9:00-11:00 Lecture 2: Genomes and alignment principles PowerPoint or PDF or PDF_handout format   Thu 04/09/2008 13:30-15:30 Lecture 3: Pairwise alignment PowerPoint or PDF or PDF_handout format   Mon 08/09/2008 13:30-15:30 Lecture 4 Pairwise alignment (2) and multiple sequence alignment (1) PowerPoint or PDF or PDF_handout format   Tue 09/09/2008 10:00-12:00 Lecture 5: Multiple alignment (2) PowerPoint or PDF or PDF_handout format   Wed 10/09/2008 9:00-11:00 Lecture 6: Homology searching PowerPoint or PDF or PDF_handout format   Thu 11/09/2008 14:00-16:00 Lecture 7: Iterative homology searching using PSI_BLAST, statistical scoring and performance evaluation PowerPoint or PDF or PDF_handout format   Wed 17/09/2008 13:30-15:30 Lecture 8: Sequence Entropy PowerPoint or PDF or PDF_handout format   Thu 18/09/2008 15:00-17:00 Lecture 9: Clustering and phylogeny PowerPoint or PDF or PDF_handout format UPGMA and NJ example or UPGMA and NJ example (handout) REST OF SCHEDULE TO BE ANNOUNCED