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 |
---|---|
Thu 28.05. | Seminar 6 (D): 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf (Reinert/Rahn) |
Fri 01.05. | bank holiday |
Thu 14.05. | bank holiday |
Thu 16.07. | Exam |
Fri 22.05. | Exercise exercise_5.pdf (Rahn) |
Tue 26.05. | Exercise exercise_6.pdf (Rahn) |
Fri 19.06. | Exercise exercise_9.pdf (Siragusa) |
Tue 23.06. | Exercise exercise_10.pdf (Siragusa) |
Tue 07.07. | Exercise exercise_11.pdf (Rahn) |
Thu 09.07. | Exercise exercise_12.pdf (Rahn) |
Tue 05.05. | Exercise exercise_3.pdf (Rahn) |
Thu 07.05. | Exercise exercise_4.pdf (Rahn) |
Fri 05.06. | Exercise exercise_7.pdf (Siragusa) |
Tue 09.06. | Exercise exercise_8.pdf (Siragusa) |
Tue 21.04. | Exercise: exercise_1_2.pdf (Reinert) |
02.06.-16.06.2015 | Filtering and approximate search in indices (Reinert/Siragusa) |
16.06.-23.06.2015 | Gapped q-grams (Reinert/Siragusa) |
Tue 19.05. | Lecture 10: BWT 1 (Reinert) |
Thu 21.05. | Lecture 11: BWT 2 (Reinert) |
Tue 02.06. | Lecture 12: Filtering methods for approximate string matching (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) |
Thu 04.06. | Lecture 13: Hierarchical filters (Reinert) |
Tue 14.04. | Lecture 1: Organisation, Rehearsal suffix array construction and search (Rahn) |
Thu 16.04. | Lecture 2: Linear time lcp computation (Reinert) |
Tue 28.04. | Lecture 3: Linear time construction with the SKEW algorithm (Reinert) |
Thu 30.04. | Lecture 4: Lazy suffix trees (Reinert) |
Tue 30.06. | Lecture 7: RNA I |
Thu 02.07. | Lecture 8: RNA II |
Fri 03.07. | Lecture 8: RNA II |
Tue 14.07. | Q&A |
Fri 24.04. | Review 1 |
Fri 15.05. | Review 2 |
Fri 29.05. | Review 3 |
Fri 12.06. | Review 4 |
Fri 26.06. | Review 5 |
30.06.-14.07.2015 | RNA analysis (by Knut Reinert) |
Thu 23.04. | Seminar 1 (A) : Two Space Saving Tricks for Linear Time LCP Array Computation (Reinert) |
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 11.06. | Seminar 7 (F): 2009_Russo_Indexed_hierarchical_approximate_string_matching.pdf.pdf (Siragusa) |
Thu 25.06. | Seminar 7 (F): PatternhunterII.pdf |
Fri 10.07. | Seminar 8: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization |
28.04.-15.05.2015 | Suffix arrays: construction (Reinert/Rahn) |
14.04.-24.04.2015 | Suffix arrays: searching with lcp array (Reinert/Rahn) |
19.05.-30.06.2015 | The BWT: searching in the FM index (Reinert/Rahn) |
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xxx | xx,0 | |||||
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xxx | xx,0 |
Date & Time | Student |
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