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TDT4287 Algorithms for bioinformatics - Autumn 2013

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Lectures

The first lecture is Wednesday 2013-08-28.

  • Lectures Wednesdays 12:15 - 14:00 in F3.
  • Exercise lectures Tuesdays 16:15 - 19:00 in F2.
  • Exercise lectures Tuesdays 16:15 - 19:00 (weeks 38-43) in K25(map).

The following plan is tentative and will be updated throughout the course.

Week Wednesday Lecturer Note Tuesday Exercise
35 Introduction PS
36 Alignment PS Chps. 6.4-6.9 in Jones & Pevzner Exercise 1
37 Heuristic alignment PS Chps. 9.3, 9.6-9.8 in Jones & Pevzner Solution exercise 1
38 Substring indexes PS Chps. 9.4-9.5 in Jones & Pevzner; Handouts (available on itslearning). BLAST/Statistical analysis Exercise 2
39 Suffix tree applications PS Chps. 9.4-9.5 in Jones & Pevzner; Handouts. Substring indexes
40 Project infoAlignment 2 PS Chps. 5.5, 12.2-12.3; 6.10, 7.2-7.4 in Jones & Pevzner Suffix tree applications,Solution ex. 2
41 Motif discovery PS Chps. 4.4-4.9, 12.2-12.3 in Jones & Pevzner
42 Motif discovery - ctd. PS Exercise 3
43 Sequencing and assembly PS Chps. 8.1-8.9 in Jones & Pevzner Solution ex. 3 Exercise 4: From Jones & Pevzner: 8.1, 8.2, 8.6, 8.9, 8.12.
44 Markov Chains PS Handouts; Ewens and Grant Q&A session (project, Ex. 3) Exercise 5
45 Hidden Markov Models PS Ewens and Grant Project (Deadline Wednesday Nov. 6 @ 24:00) Exercise 6
46 HMMs continued PS Project presentation (16:15 - 19:00 in F2; Deadline Monday Nov. 11 @ 12:00; )
47 RNA secondary structure prediction PS Chps. 5.1-5.4; 6.11-6.14 in Jones & Pevzner; Article 1 Article 2 Solution exercise 6
48 PS Q&A session
51 Exam

Project

The mandatory project presentation will be on Tuesday November 12. Each of you should prepare a presentation (for example, 6 Powerpoint slides) of your methods and results. Please send me your presentations by Monday November 11 at 12:00. The deadline for the submitting the project report is Wednesday November 6 at 24:00.

Curriculum

Jones & Pevzner - An introduction to bioinformatics algorithms


Courses similar to this one are held in other universities (ie. here and here) The lecture notes from the given courses can be used as support literature. Please note that this is not part of the curriculum.

Previous years

Exam

Place: To be announced.
Time: 2012-12-21 09:00 (4 hours)

The written examination will be in English, and it has code D. This means (page 43/352 in Studenthaandboka) that No printed or handwritten material is allowed. A specific (HP30S) calculator is allowed used. If anyone insists that the examination should be written also in Norwegian, please notify, no later than November 20.

Old exams

Please note that the curriculum has changed significantly between 2006 and 2007.

Year Exam Solution
2013 PDF PDF
2012 PDF PDF
2011 PDF
2010 PDF
2009 PDF PDF
2008 PDF PDF
2007 PDF PDF
2006 PDF PDF
Example 2006 PDF PDF

Staff

Course organiser: Pål Sætrom
Lecturers: PS: Pål Sætrom
EC: Eivind Coward

For general questions, use the mailing list: tdt4287@idi.ntnu.no.