Sequence Analysis, SoSe 2015
(LV-Nr. 19401601 (V), 19401602 (Ü), 19401611 (S)) Welcome to the Wiki of 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 excercises you will work out details 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
- Lecture on 2 July starts at 12h30.
- please read through the quasar.pdf here
- Exercise was moved to 12-14h, Arnimallee 6, SR 025/026 (cf. table below).
- Exercise on 23 April starts at 12h30.
Times and rooms
| Event | Day | Time | Address | Room | LV-No. |
|---|---|---|---|---|---|
| Lecture | Tuesday | 10-12 | Takustr. 9 | SR 051 | 19401601 |
| Exercise | Thursday | 12-14 | Arnimallee 6 | SR 025/26 | 19401602 |
| Seminar | Friday | 14-16 | Takustr. 9 | SR 005 | 19401611 |
Seminar groups
| A | B | C | E | F |
|---|---|---|---|---|
| Grahl | Buntrock | Güttler | Jahnel |
Schedule
| Date | Lecture |
|---|---|
| 14.04.-24.04.2015 | Suffix arrays: searching with lcp array (Reinert/Rahn) |
| Tue 14.04. | Lecture 1: Organisation, Rehearsal suffix array construction and search (Rahn) |
| Thu 16.04. | Lecture 2: Linear time lcp computation (Reinert) |
| Tue 21.04. | Exercise: exercise_1_2.pdf (Reinert) |
| Thu 23.04. | Seminar 1 (A) : Two Space Saving Tricks for Linear Time LCP Array Computation (Reinert) |
| Fri 24.04. | Review 1 |
| 28.04.-15.05.2015 | Suffix arrays: construction (Reinert/Rahn) |
| Tue 28.04. | Lecture 3: Linear time construction with the SKEW algorithm (Reinert) |
| Thu 30.04. | Lecture 4: Lazy suffix trees (Reinert) |
| Fri 01.05. | bank holiday |
| Tue 05.05. | Exercise exercise_3.pdf (Rahn) |
| Thu 07.05. | Exercise exercise_4.pdf (Rahn) |
| Fri 08.05. | Seminar 2 (B): DisLex a transformation for discontiguous suffix array construction (Reinert/Rahn) |
| Tue 12.05. | Seminar 3 (C): An incomplex algorithm for fast suffix array construction (Reinert/Rahn) |
| Thu 14.05. | bank holiday |
| Fri 15.05. | Review 2 |
| 19.05.-30.06.2015 | The BWT: searching in the FM index (Reinert/Rahn) |
| Tue 19.05. | Lecture 10: BWT 1 (Reinert) |
| Thu 21.05. | Lecture 11: BWT 2 (Reinert) |
| Fri 22.05. | Exercise exercise_5.pdf (Rahn) |
| Tue 26.05. | Exercise exercise_6.pdf (Rahn) |
| Thu 28.05. | Seminar 6 (D): 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf (Reinert/Rahn) |
| Fri 29.05. | Review 3 |
| 02.06.-16.06.2015 | Filtering and approximate search in indices (Reinert/Siragusa) |
| Tue 02.06. | Lecture 12: Filtering methods for approximate string matching (Siragusa) |
| Thu 04.06. | Lecture 13: Hierarchical filters (Reinert) |
| Fri 05.06. | Exercise exercise_7.pdf (Siragusa) |
| Tue 09.06. | Exercise exercise_8.pdf (Siragusa) |
| Thu 11.06. | Seminar 7 (F): 2009_Russo_Indexed_hierarchical_approximate_string_matching.pdf.pdf (Siragusa) |
| Fri 12.06. | Review 4 |
| 16.06.-23.06.2015 | Gapped q-grams (Reinert/Siragusa) |
| Tue 16.06. | Lecture 12: Gapped q-grams I: filtration schemes and thresholds (Reinert) |
| Thu 18.06. | Lecture 13: Gapped q-grams I: Specificity (Reinert) |
| Fri 19.06. | Exercise exercise_9.pdf (Siragusa) |
| Tue 23.06. | Exercise exercise_10.pdf (Siragusa) |
| Thu 25.06. | Seminar 7 (F): PatternhunterII.pdf |
| Fri 26.06. | Review 5 |
| 30.06.-14.07.2015 | RNA analysis (by Knut Reinert) |
| Tue 30.06. | Lecture 7: RNA I |
| Thu 02.07. | Lecture 8: RNA II |
| Fri 03.07. | Lecture 8: RNA II |
| Tue 07.07. | Exercise exercise_11.pdf (Rahn) |
| Thu 09.07. | Exercise exercise_12.pdf (Rahn) |
| Fri 10.07. | Seminar 8: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization |
| Tue 14.07. | Q&A |
| Thu 16.07. | Exam |
Mailing List
Sign up for the mailing list: https://lists.fu-berlin.de/listinfo/seqan-ss2015Reviews
| Matrikelnummer | points 1 | points 2 | points 3 | points 4 | points 5 | current percentage |
|---|---|---|---|---|---|---|
| xxx911 | 8,5 | 12,5 | 15 | 7 | 17 | 60,0 |
| xxx198 | 15 | 0 | 19 | 17 | 0 | 51,0 |
| xxx956 | 3 | 12 | 20 | 15 | 17 | 67,0 |
| xxx476 | 0 | 7 | 15 | 14 | 7 | 50,0 |
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.
Prüfungstermine
15.07.2015, T9 012 17.07.2015,T9 012| Time | Student |
|---|---|
| 15.7: 9:00 | Buntrock |
| 15.7: 9:30 | Güttler |
| 15.7: 10:00 | Grahl |
| 17:7: 11:00 | Jahne |
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