Sequence Analysis SS 2013

Welcome to the Wiki of the Lecture 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 ecercises you will work out details prepare 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

According to the Prüfungsordnung, the exams are ORAL !!! Please look below for your time slot on Friday

The Exercise on Tuesday 16.4.2013 will take place in SR032, Arnimallee 6

The lecture on Thursday 4.7.2013 will start 10:30

Times and rooms

Rooms and timings

Event Day Time Address Room
Lecture (until June 4th) Tuesday 10-12 Takustr. 9 SR 005
Lecture (after June 4th) Tuesday 10-12 Arnimallee 6 SR 032
Exercise (until June 6th) Thursday 10-12 Takustr. 9 SR 005
Exercise (after June 6th) Thursday 10-12 Takustr. 9 SR 053
Seminar Friday 14-16 Takustr. 9 SR 005

Schedule

Date Lecture
09.04.-19.04. Suffix arrays: searching with lcp array
09.04.2013 Lecture 1: Organisation, Rehearsal suffix array construction and search
11.04.2013 Lecture 2: Linear time lcp computation (Kasai)
12.04.2013 Exercise exercise_1+2.pdf
16.04.2013 Exercise (see Exercise 1)
18.04.2013 Seminar 1 (A): Two Space Saving Tricks for Linear Time LCP Array Computation (Manzini)
19.04.2013 Review 1  
23.04.-09.05. Suffix arrays: construction
23.04.2013 Lecture 3: Linear time construction with the SKEW algorithm
25.04.2013 Lecture 4: Lazy suffix trees
26.04.2013 Exercise exercise_3.pdf
30.04.2013 Exercise exercise_4.pdf
02.05.2013 Seminar 2 (B): DisLex a transformation for discontiguous suffix array construction
03.05.2013 Seminar 3 (A): An incomplex algorithm for fast suffix array construction
07.05.2013 Review 2  
10.05.-22.05. Suffix arrays: navigating
10.05.2013 Lecture 5: Enhanced suffix arrays 1
14.05.2013 Lecture 6: Enhanced suffix arrays 2
16.05.2013 Exercise exercise_5.pdf
17.05.2013 Exercise
21.05.2013 Seminar 5 (A/B): Replacing suffix trees with enhanced suffix arrays
23.05.2013 Review 3  
24.05.-07.06. The BWT: searching in the FM index
24.05.2013 Lecture 7: BWT 1
28.05.2013 Lecture 8: BWT 2
30.05.2013 Exercise exercise_6.pdf
31.06.2013 Exercise
04.06.2013 Seminar 6 (B): High throughput short read alignment via bi-directional BWT
06.06.2013 Review 4  
07.06.-20.06. Filtering and approximate search in indices
07.06.2013 Lecture 9: Filter algorithms
11.06.2013 Lecture 10: Filter algorithms and approximate index search
13.06.2013 Exercise
14.06.2013 Exercise exercise_7.pdf
18.06.2013 Seminar 7 (A+B): Masai.pdf
20.06.2013 Review 5  
21.06.-25.06. RNA analysis
25.06.2013 Lecture 11: RNA I
27.06.2013 Exercise
28.06.2013 Exercise exercise_8.pdf
02.07.2013 Review 5  
04.07.-12.07 Genome comparison
04.07.2013 Lecture 12: Genome comparison I
05.07.2013 Lecture 13: Genome comparison II
09.07.2013 Exercise exercise_9.pdf
11.07.2013 Exercise
12.07.2013 Exam

Seminar Groups

Group A Group BSorted ascending
Matzig Eckert
Phieler Hesse
Schmoldt Martens

Mailing List

Sign up for the mailing list: https://lists.fu-berlin.de/listinfo/SequenceAnalysis2013/

Reviews

Requirements for Aktive Teilnahme

  • You have to be prepared to give a seminar talk (if its your groups turn).
  • In addition you need to reach 50% of all points of the reviews.

Seminar papers

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Topic revision: 11 Jul 2013, SandroAndreotti