Sequence Analysis, SoSe 2016

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

Welcome to the Wiki of Sequence Analysis.

Dear Students. We will use for the lecture the new KVV system. Please sign up here

THIS 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.

News

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Times and rooms

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

Seminar groups

A	B	C	E	F

Schedule (noch alt)

Date	Lecture
19.05.-30.06.2015	The BWT: searching in the FM index (Reinert/Rahn)
14.04.-24.04.2015	Suffix arrays: searching with lcp array (Reinert/Rahn)
28.04.-15.05.2015	Suffix arrays: construction (Reinert/Rahn)
Fri 10.07.	Seminar 8: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
Thu 25.06.	Seminar 7 (F): PatternhunterII.pdf
Thu 11.06.	Seminar 7 (F): 2009_Russo_Indexed_hierarchical_approximate_string_matching.pdf.pdf (Siragusa)
Tue 12.05.	Seminar 3 (C): An incomplex algorithm for fast suffix array construction (Reinert/Rahn)
Fri 08.05.	Seminar 2 (B): DisLex a transformation for discontiguous suffix array construction (Reinert/Rahn)
Thu 23.04.	Seminar 1 (A) : Two Space Saving Tricks for Linear Time LCP Array Computation (Reinert)
30.06.-14.07.2015	RNA analysis (by Knut Reinert)
Fri 26.06.	Review 5
Fri 12.06.	Review 4
Fri 29.05.	Review 3
Fri 15.05.	Review 2
Fri 24.04.	Review 1
Tue 14.07.	Q&A
Thu 02.07.	Lecture 8: RNA II
Fri 03.07.	Lecture 8: RNA II
Tue 30.06.	Lecture 7: RNA I
Thu 30.04.	Lecture 4: Lazy suffix trees (Reinert)
Tue 28.04.	Lecture 3: Linear time construction with the SKEW algorithm (Reinert)
Thu 16.04.	Lecture 2: Linear time lcp computation (Reinert)
Tue 14.04.	Lecture 1: Organisation, Rehearsal suffix array construction and search (Rahn)
Thu 04.06.	Lecture 13: Hierarchical filters (Reinert)
Thu 18.06.	Lecture 13: Gapped q-grams I: Specificity (Reinert)
Tue 16.06.	Lecture 12: Gapped q-grams I: filtration schemes and thresholds (Reinert)
Tue 02.06.	Lecture 12: Filtering methods for approximate string matching (Siragusa)
Thu 21.05.	Lecture 11: BWT 2 (Reinert)
Tue 19.05.	Lecture 10: BWT 1 (Reinert)
16.06.-23.06.2015	Gapped q-grams (Reinert/Siragusa)
02.06.-16.06.2015	Filtering and approximate search in indices (Reinert/Siragusa)
Tue 21.04.	Exercise: exercise_1_2.pdf (Reinert)
Tue 09.06.	Exercise exercise_8.pdf (Siragusa)
Fri 05.06.	Exercise exercise_7.pdf (Siragusa)
Thu 07.05.	Exercise exercise_4.pdf (Rahn)
Tue 05.05.	Exercise exercise_3.pdf (Rahn)
Thu 09.07.	Exercise exercise_12.pdf (Rahn)
Tue 07.07.	Exercise exercise_11.pdf (Rahn)
Tue 23.06.	Exercise exercise_10.pdf (Siragusa)
Fri 19.06.	Exercise exercise_9.pdf (Siragusa)
Tue 26.05.	Exercise exercise_6.pdf (Rahn)
Fri 22.05.	Exercise exercise_5.pdf (Rahn)
Thu 16.07.	Exam
Fri 01.05.	bank holiday
Thu 14.05.	bank holiday
Thu 28.05.	Seminar 6 (D): 2009_Lam_High_throughput_short_read_alignment_via_bi-directional_BWT.pdf (Reinert/Rahn)

Mailing List

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

Reviews

Matrikelnummer	points 1	points 2	points 3	points 4	points 5	current percentage
xxx						xx,0
xxx						xx,0
xxx						xx,0
xxx						xx,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

xx.07.2016, xx.07.2016,

Date & Time	Student