Welcome to the Wiki of Sequence Analysis.
Dear Students. We will use for the lecture the new KVV system. Please sign up hereTHIS IS OLD
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.
Event | Day | Time | Address | Room | LV-No. |
---|---|---|---|---|---|
Lecture | Tuesday | 10-12 | Takustr. 9 | SR 051 | 19401601 |
Exercise | Thursday | 12-14 | Arnimallee 3 | SR 005 | 19401602 |
Seminar | Friday | 14-16 | Takustr. 9 | SR 005 | 19401611 |
A | B | C | E | F |
---|---|---|---|---|
Date | Lecture |
---|---|
02.06.-16.06.2015 | Filtering and approximate search in indices (Reinert/Siragusa) |
14.04.-24.04.2015 | Suffix arrays: searching with lcp array (Reinert/Rahn) |
16.06.-23.06.2015 | Gapped q-grams (Reinert/Siragusa) |
19.05.-30.06.2015 | The BWT: searching in the FM index (Reinert/Rahn) |
28.04.-15.05.2015 | Suffix arrays: construction (Reinert/Rahn) |
30.06.-14.07.2015 | RNA analysis (by Knut Reinert) |
Fri 01.05. | bank holiday |
Fri 03.07. | Lecture 8: RNA II |
Fri 05.06. | Exercise exercise_7.pdf (Siragusa) |
Fri 08.05. | Seminar 2 (B): DisLex a transformation for discontiguous suffix array construction (Reinert/Rahn) |
Fri 10.07. | Seminar 8: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization |
Fri 12.06. | Review 4 |
Fri 15.05. | Review 2 |
Fri 19.06. | Exercise exercise_9.pdf (Siragusa) |
Fri 22.05. | Exercise exercise_5.pdf (Rahn) |
Fri 24.04. | Review 1 |
Fri 26.06. | Review 5 |
Fri 29.05. | Review 3 |
Thu 02.07. | Lecture 8: RNA II |
Thu 04.06. | Lecture 13: Hierarchical filters (Reinert) |
Thu 07.05. | Exercise exercise_4.pdf (Rahn) |
Thu 09.07. | Exercise exercise_12.pdf (Rahn) |
Thu 11.06. | Seminar 7 (F): 2009_Russo_Indexed_hierarchical_approximate_string_matching.pdf.pdf (Siragusa) |
Thu 14.05. | bank holiday |
Thu 16.04. | Lecture 2: Linear time lcp computation (Reinert) |
Thu 16.07. | Exam |
Thu 18.06. | Lecture 13: Gapped q-grams I: Specificity (Reinert) |
Thu 21.05. | Lecture 11: BWT 2 (Reinert) |
Thu 23.04. | Seminar 1 (A) : Two Space Saving Tricks for Linear Time LCP Array Computation (Reinert) |
Thu 25.06. | Seminar 7 (F): PatternhunterII.pdf |
Thu 28.05. | Seminar 6 (D): 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf (Reinert/Rahn) |
Thu 30.04. | Lecture 4: Lazy suffix trees (Reinert) |
Tue 02.06. | Lecture 12: Filtering methods for approximate string matching (Siragusa) |
Tue 05.05. | Exercise exercise_3.pdf (Rahn) |
Tue 07.07. | Exercise exercise_11.pdf (Rahn) |
Tue 09.06. | Exercise exercise_8.pdf (Siragusa) |
Tue 12.05. | Seminar 3 (C): An incomplex algorithm for fast suffix array construction (Reinert/Rahn) |
Tue 14.04. | Lecture 1: Organisation, Rehearsal suffix array construction and search (Rahn) |
Tue 14.07. | Q&A |
Tue 16.06. | Lecture 12: Gapped q-grams I: filtration schemes and thresholds (Reinert) |
Tue 19.05. | Lecture 10: BWT 1 (Reinert) |
Tue 21.04. | Exercise: exercise_1_2.pdf (Reinert) |
Tue 23.06. | Exercise exercise_10.pdf (Siragusa) |
Tue 26.05. | Exercise exercise_6.pdf (Rahn) |
Tue 28.04. | Lecture 3: Linear time construction with the SKEW algorithm (Reinert) |
Tue 30.06. | Lecture 7: RNA I |
Matrikelnummer | points 1 | points 2 | points 3 | points 4 | points 5 | current percentage |
---|---|---|---|---|---|---|
xxx | xx,0 | |||||
xxx | xx,0 | |||||
xxx | xx,0 | |||||
xxx | xx,0 |
Date & Time | Student |
---|---|