Sequence Analysis SS 2013
Welcome to the Wiki of the Lecture Sequence Analysis. This module consists of 2 hours lecture, 2 hours exercise and 2 hours seminar. The form will be in blocks, in which you will hear about certain aspects of sequence analysis in the lecture, then in the ecercises you will work out details prepare for the seminar.
In the seminar we will all talk about an original paper connected to the topic (discussion leaders will be chosen by a draw) and afterwards have a short review exam for the block. Students will be in two groups (A and B) which will take turn in giving seminar talks.
Each block is finished by a review.
For the exam the content of the seminar papers AND lectures will be relevant.
News
According to the Prüfungsordnung, the exams are ORAL !!! Please look below for your time slot on Friday The Exercise on Tuesday 16.4.2013 will take place in SR032, Arnimallee 6 The lecture on Thursday 4.7.2013 will start 10:30Times and rooms
Rooms and timings
| Event | Day | Time | Address | Room |
|---|---|---|---|---|
| Lecture (until June 4th) | Tuesday | 10-12 | Takustr. 9 | SR 005 |
| Lecture (after June 4th) | Tuesday | 10-12 | Arnimallee 6 | SR 032 |
| Exercise (until June 6th) | Thursday | 10-12 | Takustr. 9 | SR 005 |
| Exercise (after June 6th) | Thursday | 10-12 | Takustr. 9 | SR 053 |
| Seminar | Friday | 14-16 | Takustr. 9 | SR 005 |
Schedule
| Date | Lecture | |
|---|---|---|
| 09.04.-19.04. | Suffix arrays: searching with lcp array | |
| 09.04.2013 | Lecture 1: Organisation, Rehearsal suffix array construction and search | |
| 11.04.2013 | Lecture 2: Linear time lcp computation (Kasai) | |
| 12.04.2013 | Exercise exercise_1+2.pdf | |
| 16.04.2013 | Exercise (see Exercise 1) | |
| 18.04.2013 | Seminar 1 (A): Two Space Saving Tricks for Linear Time LCP Array Computation (Manzini) | |
| 19.04.2013 | Review 1 | |
| 23.04.-09.05. | Suffix arrays: construction | |
| 23.04.2013 | Lecture 3: Linear time construction with the SKEW algorithm | |
| 25.04.2013 | Lecture 4: Lazy suffix trees | |
| 26.04.2013 | Exercise exercise_3.pdf | |
| 30.04.2013 | Exercise exercise_4.pdf | |
| 02.05.2013 | Seminar 2 (B): DisLex a transformation for discontiguous suffix array construction | |
| 03.05.2013 | Seminar 3 (A): An incomplex algorithm for fast suffix array construction | |
| 07.05.2013 | Review 2 | |
| 10.05.-22.05. | Suffix arrays: navigating | |
| 10.05.2013 | Lecture 5: Enhanced suffix arrays 1 | |
| 14.05.2013 | Lecture 6: Enhanced suffix arrays 2 | |
| 16.05.2013 | Exercise exercise_5.pdf | |
| 17.05.2013 | Exercise | |
| 21.05.2013 | Seminar 5 (A/B): Replacing suffix trees with enhanced suffix arrays | |
| 23.05.2013 | Review 3 | |
| 24.05.-07.06. | The BWT: searching in the FM index | |
| 24.05.2013 | Lecture 7: BWT 1 | |
| 28.05.2013 | Lecture 8: BWT 2 | |
| 30.05.2013 | Exercise exercise_6.pdf | |
| 31.06.2013 | Exercise | |
| 04.06.2013 | Seminar 6 (B): High throughput short read alignment via bi-directional BWT | |
| 06.06.2013 | Review 4 | |
| 07.06.-20.06. | Filtering and approximate search in indices | |
| 07.06.2013 | Lecture 9: Filter algorithms | |
| 11.06.2013 | Lecture 10: Filter algorithms and approximate index search | |
| 13.06.2013 | Exercise | |
| 14.06.2013 | Exercise exercise_7.pdf | |
| 18.06.2013 | Seminar 7 (A+B): Masai.pdf | |
| 20.06.2013 | Review 5 | |
| 21.06.-25.06. | RNA analysis | |
| 25.06.2013 | Lecture 11: RNA I | |
| 27.06.2013 | Exercise | |
| 28.06.2013 | Exercise exercise_8.pdf | |
| 02.07.2013 | Review 5 | |
| 04.07.-12.07 | Genome comparison | |
| 04.07.2013 | Lecture 12: Genome comparison I | |
| 05.07.2013 | Lecture 13: Genome comparison II | |
| 09.07.2013 | Exercise exercise_9.pdf | |
| 11.07.2013 | Exercise | |
| 12.07.2013 | Exam | |
Seminar Groups
| Group A | Group B |
|---|---|
| Phieler | Hesse |
| Schmoldt | Martens |
| Matzig | Eckert |
Mailing List
Sign up for the mailing list: https://lists.fu-berlin.de/listinfo/SequenceAnalysis2013/Reviews
Requirements for Aktive Teilnahme
- You have to be prepared to give a seminar talk (if its your groups turn).
- In addition you need to reach 50% of all points of the reviews.
Seminar papers
- DisLex a transformation for discontiguous suffix array construction: Seminar paper 2
- An incomplex algorithm for fast suffix array construction: Seminar paper 3
- Bidirectional search in a string with wavelet trees and bidirectional matching statistics: Seminar 5
- 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf: 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf
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