# Forside

## Innhold

## TDT4287 Algorithms for bioinformatics - Autumn 2013

You should follow the TDT4287 information channel.

## Last news

- Please follow the information channel for all news.

## 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

- Introduction
- Substring indexes
- Gusfield. "Algorithms on strings, trees, and sequences: Computer science and computational biology". Chapters 5, 6.1, 7.1-7.6, and 7.8-7.10. (Copies will be handed out during the lecture. )

- RNA secondary structure prediction
- Markov Chains and Hidden Markov Models
- Ewens and Grant Statistical Methods in Bioinformatics. Parts of Chapters 4, 10 and 11.
- Background in probability theory: Sections 1.2-1.5, 1.12 and 2.1 in Ewens & Grant will cover most of what is needed for the Markov chain theory (discrete random variables, events, conditional probability).

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 | ||

2012 | ||

2011 | ||

2010 | ||

2009 | ||

2008 | ||

2007 | ||

2006 | ||

Example 2006 |

## Staff

Course organiser: | Pål Sætrom |

Lecturers: | PS: Pål Sætrom |

EC: Eivind Coward | |

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