Exam slots:
| Date/Time | Surname | First name | |
| 19.7.: 10:00 | Kmiecinski | Rene Wesley | |
| 20.7.: 9:30 | Shao | Zhiao | |
| 20.7: 11:00 | Musch | Vincent | |
| 20.7: 11:30 | Glöde | Svenja | |
| 20.7.: 13:30 | Zandvakili | Aboozar | |
| 20.7.: 14:00 | Bannwitz | Dominik | |
| 20.7.: 14:30 | Wild | Nora |
This is a mandatory course for students in the MSc Bioinformatics.
The module consists of a lecture, a seminar, and exercises which will be blocked according to the respective topic. This means we will have first several lectures, followed by exercises, followed by seminars. One block is concluded with a review test about the content.
Content: Requirements for "aktive Teilnahme":
- You have to be prepared to give a seminar talk (if it's your group's turn).
- In addition, you need to reach 50% of all points of the reviews.
- Submit homework solutions (only one upload per group required)
Contact:
- knut.reinert@fu-berlin.de
- svenja.mehringer@fu-berlin.de
- s.gottlieb@fu-berlin.de (If you have any questions, write me!, or come to T9/R010)
Location
Tuesdays: A3/SR 119
Thursdays: T9/055 Seminarraum
Content
There are corresponding lecture videos from SS 2023 and SS 2022.
| # | Date | Event |
|---|---|---|
| 1 | 18.04. | L: Suffix array search |
| 2 | 18.04. | L: LCP computation |
| 3 | 20.04. | L: Suffix array construction |
| 4 | 25.04. | Exercise |
| 5 | 25.04. | Exercise |
| 6 | 27.04. | Exercise |
| 7 | 02.05. | S: DisLex: a transformation for discontiguous suffix array construction (G1) |
| 8 | 02.05. | Review 1 |
| 9 | 04.05. | L: Onedirectional FM-indices |
| 10 | 09.05. | L: Bidirectional FM-indices |
| 11 | 09.05. | L: Extensions of FM-indices |
| 12 | 11.05. | Exercise |
| 13 | 16.05. | Exercise |
| 14 | 16.05. | S: FM-trees (G2) |
| 15 | 18.05 | Holiday |
| 16 | 23.05 | Review 2 |
| 17 | 23.05. | L: k-mer based analysis I: Concentration bounds |
| 18 | 25.05. | L: k-mer based analysis II: Estimate cardinalities and minimizers |
| 19 | 30.05. | Exercise (2x) |
| 20 | 01.06. | Exercise |
| 21 | 06.06. | L: k-mer based analysis III: Storing sets of kmers |
| 22 | 06.06. | L: k-mer based analysis IV: Storing sets of sets of k-mers and sketching |
| 23 | 08.06. | L: k-mer based analysis V: Comparison of sets k-mers |
| 24 | 13.06. | Exercise |
| 25 | 13.06. | Exercise |
| 26 | 15.06. | S: Strobemers: Effective sequence similarity detection ... (G3) |
| 27 | 20.06. | Review 3 |
| 28 | 20.06. | L: Filter I |
| 29 | 22.06. | L: Filter II |
| 30 | 27.06 | L: Filter III |
| 31 | 27.06. | L: Filter IV: Verification: Myers Bitvector Algorithm |
| 32 | 29.06. | Exercise |
| 33 | 04.07. | Exercise |
| 34 | 04.07. | Exercise |
| 35 | 06.07. | S: Genmap (G4) |
| 36 | 11.07. | S: Adaptive Seeds (G?) |
| 37 | 11.07. | Review 4 |
| 38 | 13.07. | Q&A |
| 39 | 20.07. | Exams |