Sequence Analysis, SoSe 2014

(LV-Nr. 19716, 19716a, 19716b)

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

  • Results of the 4th review are online
  • On Friday, July 4th the lecture starts at 2:00 pm (s.t.)
  • Results of the 3rd review are online
  • interesting thoughts concerning oral exams
  • Results 2nd review are online
  • New mailing lst is now open
  • According to the Prüfungsordnung, the exams are ORAL!!!
  • Prof. Clote had to return to the US due to personal reasons. Hence the plan for the RNA block is changed.

Times and rooms

Event Day Time Address Room
Lecture Tuesday 10-12 Takustr. 9 SR 051
Exercise Thursday 10-12 Takustr. 9 SR 055
Seminar Friday 14-16 Takustr. 9 SR 005

Seminar groups

A B C E F
Bierling Bressin Budach Faizi Godschan
Kokatjuhha Lekschas Liedtke Roskosch Schulze
Hamid Strauch Dadi Alberdi Güttler
      Pockrandt Peschutter
  Klamka   Ebeling  

Schedule

Date Lecture
15.04.-25.04. Suffix arrays: searching with lcp array (Knut Reinert)
15.04.2014 Lecture 1: Organisation, Rehearsal suffix array construction and search
17.04.2014 Lecture 2: Linear time lcp computation (Kasai)
22.04.2014 Exercise: exercise_1_2.pdf
24.04.2014 Seminar 1 (A) : Two Space Saving Tricks for Linear Time LCP Array Computation
25.04.2014 Review 1  
29.04.-15.05. Suffix arrays: construction (Knut Reinert)
29.04.2014 Lecture 3: Linear time construction with the SKEW algorithm
02.05.2014 Lecture 4: Lazy suffix trees
06.05.2014 Exercise exercise_3.pdf
08.05.2014 Exercise exercise_4.pdf
09.05.2014 Seminar 2 (B): DisLex a transformation for discontiguous suffix array construction
13.05.2014 Seminar 3 (B): An incomplex algorithm for fast suffix array construction
15.05.2014 Review 2  
16.05.-03.06. Suffix arrays: navigating (David Weese)
16.05.2014 Lecture 5: Enhanced suffix arrays 1
20.05.2014 Lecture 6: Enhanced suffix arrays 2
22.05.2014 Exercise exercise_5.pdf
23.05.2013 Exercise
27.05.2013 Seminar 4 (C): Wee LCP
30.05.2014 Review 3  
03.06.-17.06. RNA analysis (by Knut Reinert/David Weese)
03.06.2014 Lecture 7: RNA I
05.06.2014 Lecture 8: RNA II
06.06.2014 canceled
10.06.2014 canceled
12.06.2014 Exercise I exercise_6.pdf
13.06.2014 canceled
17.06.2014 Review 4  
19.06.-01.07. The BWT: searching in the FM index (Knut Reinert)
19.06.2014 Lecture 10: BWT 1
20.06.2014 Lecture 11: BWT 2
24.06.2014 Exercise exercise_7.pdf
26.06.2014 Exercise
27.06.2014 Seminar 6 (E): 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf
01.07.2014 Review 5
03.07.-15.07. Filtering and approximate search in indices (David Weese)
03.07.2014 Lecture 12: Filter algorithms
04.07.2014 Lecture 13: Filter algorithms and approximate index search
08.07.2014 Exercise
10.07.2014 Exercise exercise_8.pdf
11.07.2014 Seminar 7 (F): Masai.pdf und/oder 2009_Russo_Indexed_hierarchical_approximate_string_matching.pdf.pdf
15.07.2014 Questions and Answers
17.07.2014 Exam

Mailing List

Sign up for the mailing list: https://lists.fu-berlin.de/listinfo/seqan-ss2014

Reviews

Matrikelnummer points 1 points 2 points 3 points 4 current percentage
xxxx1779 5 / 20 14 / 20 14 / 20 10/20 53.8
xxxx0719 13 / 20 14 / 20 15 / 20 20/20 77.5
xxxx5180 1 / 20 0 / 20 0 / 20 0/20 1.3
xxxx4374 8 / 20 20 / 20 15 / 20 16/20 73.8
xxxx4257 20 / 20 14 / 20 15 / 20 20/20 86.3
xxxx6435 12 / 20 16 / 20 12 / 20 15/20 68.8
xxxx3802 9 / 20 19 / 20 14 / 20 18/20 75.0
xxxx8435 15 / 20 10 / 20 15 / 20 20/20 75.0
xxxx8784 7 / 20 17 / 20 10 / 20 16/20 62.5
xxxx8808 14 / 20 15 / 20 19 / 20 20/20 85.0
xxxx4686 11 / 20 16 / 20 19 / 20 20/20 82.5
xxxx5235 5 / 20 15 / 20 9 / 20 15/20 55.0
xxxx3598 20 / 20 20 / 20 19 / 20 20/20 98.8
xxxx7260 15 / 20 17 / 20 14 / 20 20/20 82.5
xxxx5606 20 / 20 16 / 20 17 / 20 20/20 91.3
xxxx0956 2 / 20 5 / 20 8 / 20 7/20 27.5
xxxx2952 --- / --- 12 / 20 18 / 20 20/20 82.4

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

17.7.2014, T9 012

Time Student
Pockrandt 8:40
Bierling 9:00
Bressin 9:20
Budach 9:40
Faizi 10:00
Godschan 10:20
Kokatjuhha 10:40
Lekschas 11:00
Lunchbreak  
Liedtke 13:00
Roskosch 13:20
Schulze 13:40
Strauch 14:00
Alberdi 14:20
Güttler 14:40
Peschutter 15:20
Klamka 15:40
Ebeling 16:00
Hamid 16:20
Topic revision: r32 - 12 Jul 2014, KnutReinert
 
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