Information for students
This is an elective course (Wahlpflichtveranstaltung) for students in the MSc Bioinformatics. As opposed to the recent years, we will use the KVV Sakai system as an exchange platform.
The modul consists of a lecture, a seminar and exercises which will be blocked according to the respective optic. 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: We will deal with methods for approximate searching and variant detection in sequences, the construction and use of modern index structures and methods for RNA sequence analysis and variant detection.
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.
Seminar group A: Pluhatsch,Krüger,Gottlieb,
Seminar group B: Seiler, Dawid
Seminar group C: Kim, Heinig, Darvish
Content
| Date | Event |
|---|---|
| 17.4. | L: Organisation, Rehearsal suffix array construction and search |
| 19.4. | L: Linear time lcp computation |
| 20.4. | Exercise |
| 24.4. | S: Two Space Saving Tricks for Linear Time LCP Array Computation (A) |
| 26.4. | Review 1 |
| 27.4. | L: Linear time construction with the SKEW algorithm |
| 3.5. | L: Lazy suffix trees |
| 4.5. | Exercise |
| 8.5. | S: DisLex a transformation for discontiguous suffix array construction (B) |
| 10.5. | Holiday |
| 11.5. | Exercise |
| 15.5. | S: An incomplex algorithm for fast suffix array construction (C) |
| 17.5 | Review 2 |
| 18.5 | L: Burrows Wheeler transform 1 |
| 22.5. | L: Burrows Wheeler transform 2 |
| 24.5. | L: Burrows Wheeler transform 3 |
| 25.5. | Exercise |
| 29.5. | S: FMtree: A fast locating algorithm of FM-indexes for genomic data (A) |
| 31.5. | S: HT short read alignment via the bidirectional BWT (B) |
| 1.6. | Review 3 |
| 5.6. | L: Factor filters |
| 7.6. | L: 01*0 Filter |
| 8.6. | L: Optimal search schemes |
| 12.6. | L: Counting filters |
| 14.6. | Exercise |
| 15.6. | Exercise |
| 19.6. | S: (C) 01*0 Seeds |
| 21.6. | S: (A) Adaptive seeds |
| 22.6 | Review 4 |
| 26.6. | Exercise |
| 28.6. | Myers Bitvector algorithm I |
| 29.6. | Myers Bitvector algorithm II/ |
| 3.7. | Bloom Filter / Binning directories |
| 5.7. | Exercise |
| 6.7. | S: Byte Aligned Pattern Matching (B) |
| 10.7. | Rehearsal |
| 12.7 | Review 5 |
| 13.7 | Self study |
| 17.7. | Oral examinations (13-16, 30 minute slots) (14:00 Gottlieb, 16 Uhr Kim) |
| 18.7. | Oral examinations (13-16, 30 minute slots) (13:00 Matschkowski, 13:30 Krüger, 14:00 Pluhatsch, 14:30 Seiler, 15:00 Darvish) |