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 B
Phieler	Hesse
Schmoldt	Martens
Matzig	Eckert

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

• Two Space Saving Tricks for Linear Time LCP Array Computation (Manzini): Seminar paper 1

• DisLex a transformation for discontiguous suffix array construction: Seminar paper 2

• An incomplex algorithm for fast suffix array construction: Seminar paper 3

• Replacing suffix trees with enhanced suffix arrays: Seminar 4

• Bidirectional search in a string with wavelet trees and bidirectional matching statistics: Seminar 5

• 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf: 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf