Sequence Analysis, SoSe 2015

(LV-Nr. 19401601 (V), 19401602 (Ü), 19401611 (S))

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

  • Lecture on 2 July starts at 12h30.
  • please read through the quasar.pdf here
  • Exercise was moved to 12-14h, Arnimallee 6, SR 025/026 (cf. table below).
  • Exercise on 23 April starts at 12h30.

Times and rooms

Event Day Time Address Room LV-No.
Lecture Tuesday 10-12 Takustr. 9 SR 051 19401601
Exercise Thursday 12-14 Arnimallee 6 SR 025/26 19401602
Seminar Friday 14-16 Takustr. 9 SR 005 19401611

Seminar groups

A B C E F
Grahl Buntrock Güttler Jahnel  

Schedule

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

Mailing List

Sign up for the mailing list: https://lists.fu-berlin.de/listinfo/seqan-ss2015

Reviews

Matrikelnummer points 1 points 2 points 3 points 4 points 5 current percentage
xxx911 8,5 12,5 15 7 17 60,0
xxx198 15 0 19 17 0 51,0
xxx956 3 12 20 15 17 67,0
xxx476 0 7 15 14 7 50,0

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

15.07.2015, T9 012 17.07.2015,T9 012

Time Student
15.7: 9:00 Buntrock
15.7: 9:30 Güttler
15.7: 10:00 Grahl
17:7: 11:00 Jahne

Topic attachments
I Attachment Action Size Date Who Comment
exercise_10.pdfpdf exercise_10.pdf manage 66.2 K 18 Jun 2015 - 13:48 EnricoSiragusa  
exercise_6.pdfpdf exercise_6.pdf manage 31.0 K 01 Jun 2015 - 18:20 EnricoSiragusa  
exercise_8.pdfpdf exercise_8.pdf manage 75.4 K 05 Jun 2015 - 12:07 EnricoSiragusa  
exercise_9.pdfpdf exercise_9.pdf manage 55.9 K 16 Jun 2015 - 09:12 EnricoSiragusa  
Topic revision: r38 - 07 Jul 2015, ReneMaerker
 
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