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---+!! Page %TOPIC% Welcome to the Wiki of the Lecture Advanced Algorithms in Bioinformatics (P4). ---++ News * %RED% (18.1.13) The results of the second exam can be found below%ENDCOLOR% * (24.9.12) The second exam will take place on Wednesday 24.10.12 12-14 in room SR119, Arnimallee 3%ENDCOLOR% * (14.3.12) The lecture this year will be interleaved with practical exercises that will take place in the Bioinformatik pool. ---++ Results exam 2 | *Matrikelnummer* | *points* | *mark* | |xxx343 |74.5 |1.3| |xxx956 |33 |5.0| |xxx8987 |51 |3.3| |xxx3988 |12 |5.0| |xxx4170 |39.5 |4.0| |xxx8601 |47 |3.3| |xxx539 |38 |4.0| |xxx2779 |51 |3.3| ---++ Results exam | *Matrikelnummer* | *points* | *mark* | |xxx9094 |62 |2.3| |xxx4048 |39 |4.0| |xxx9983 |0 |5.0| |xxx6803 |44 |3.7| |xxx343 |0 |5.0| |xxx2343 |0 |5.0| |xxx2041 |0 |5.0| |xxx5236 |60.5 |2.3| |xxx938 |0 |5.0| |xxx4884 |72.5 |1.7| |xxx1290 |50 |3.3| |xxx956 |24 |5.0| |xxx2428 |0 |5.0| |xxx6387 |0 |5.0| |xxx7470 |55.5 |3.0| |xxx5642 |73 |1.7| |xxx1170 |60.5 |2.3| |xxx5132 |71 |1.7| |xxx6675 |58 |2.7| |xxx8987 |0 |5.0| |xxx9136 |55 |3.0| |xxx6571 |72 |1.7| |xxx1655 |61 |2.3| |xxx8462 |58.5 |2.7| |xxx1786 |61 |2.3| |xxx3988 |30 |5.0| |xxx480 |60.5 |2.3| |xxx671 |83 |1.0| |xxx1347 |69.5 |1.7| |xxx2077 |70.5 |1.7| |xxx5795 |61.5 |2.3| |xxx4170 |19 |5.0| |xxx7727 |55 |3.0| |xxx3962 |61.5 |2.3| |xxx4177 |69.5 |1.7| |xxx6835 |66 |2.0| |xxx6104 |73 |1.7| |xxx3282 |27 |5.0| |xxx1695 |58 |2.7| |xxx2290 |78 |1.0| |xxx7304 |60.5 |2.3| |xxx6942 |65 |2.0| |xxx7315 |0 |5.0| |xxx8601 |0 |5.0| |xxx539 |0 |5.0| |xxx6179 |71.5 |1.7| |xxx4859 |75.5 |1.3| |xxx7592 |54 |3.0| |xxx1288 |41 |4.0| |xxx2779 |29|5.0| ---++ Times and rooms ---+++ Rooms and timings |*Event* | *Day* | *Time* | *Address* | *Room* | | Lecture | Tue | 10-12 | Takustr. 9 | 005 | | Lecture | Thu | 10-12 | Takustr. 9 | 005 | | Exercise | Wed | 14-16 | Arnimallee 14 | HS B (0.1.0.1) | | Practical exercises | during assignment weeks Tue, Thu | 10-12 | A2 | Bioinformatik pool | ---+++ Schedule | *Date* | *Lecture*| | 10.04.-17.04. | *Online Searching and Verification* | | 10.04.2012 | [[Lecture1Materials][Lecture 1]]: Introduction, simple Horspool and Wu-Manber algorithm | | 12.04.2012 | [[Lecture2Materials][Lecture 2]]: Shift-Or algorithm, Ukkonen trick for approximate string matching | | 17.04.2012 | [[Lecture3Materials][Lecture 3]]: Myers bitvector edit distance algorithm, banded version | | 23.04.-28.04. | *[[AssignmentWeek1][Assignment week 1]]* | | 01.05.-08.05. | *Filter Algorithms* | | 01.05.2012 | Holiday | | 03.05.2012 | [[Lecture4Materials][Lecture 4]]: Read mapping considerations | | 08.05.2012 | [[Lecture5Materials][Lecture 5]]: Pigeonhole filter and q-gram counting filter | | 10.05.2012 | [[Lecture6Materials][Lecture 6]]: q-gram counting filter II | | 14.05.-18.05 | *[[AssignmentWeek2][Assignment week 2]]* | | 22.05.-07.06. | *(Enhanced) Suffix Array and FM-index* | | 22.05.2012 | [[Lecture7Materials][Lecture 7]]: Suffix array construction and searching with lcp values | | 24.05.2012 | [[Lecture8Materials][Lecture 8]]: Suffix array construction in linear time | | 29.05.2012 | [[Lecture9Materials][Lecture 9]]: Burrows-Wheeler transform (BWT), L-to-F mapping | | 30.05.2012 | Review 1 (during exercises) | | 31.05.2012 | [[Lecture10Materials][Lecture 10]]: BWT based string searching and compression | | 05.06.2012 | [[Lecture11Materials][Lecture 11]]: Enhanced suffix arrays | | 07.06.-19.06. | *Comparative RNA analysis* | | 07.06.2012 | [[Lecture12Materials][Lecture 12]]: Comparative RNA Analysis | | 11.06.-15.06 | *[[AssignmentWeek3][Assignment week 3]]* | | 19.06.2012 | [[Lecture16Materials][Lecture 13]]: Comparative RNA Analysis II | | 21.06.-03.07. | *Genome Comparison* | | 21.06.2012 | [[Lecture17Materials][Lecture 14]]: Collinear genome comparison I: Segment match refinement | | 26.06.2012 | [[Lecture13Materials][Lecture 15]]: Collinear genome comparison II: Multiple semgent match refinement and T-Coffee | | 28.06.2012 | [[Lecture14Materials][Lecture 16]]: Non-collinear alignment: progressiveMauve | | 03.07.2012 | [[Lecture15Materials][Lecture 17]]: Genome rearrangement | | 05.07.2012 | Review 2 (during lecture) | | 10.07.2012 | Buffer || | 12.07.2012 | Exam || ---+++ Exercises | *Nr.* | *Link*| | 1 | [[%ATTACHURL%/Exercise1.pdf][Exercise1.pdf]] | | 2 | [[%ATTACHURL%/Exercise_2.pdf][Exercise2.pdf]] | | 3 | [[%ATTACHURL%/Exercise_3.pdf][Exercise3.pdf]] | | 4 | [[%ATTACHURL%/Exercise_4.pdf][Exercise4.pdf]] | | 5 | [[%ATTACHURL%/Exercise_5.pdf][Exercise5.pdf]] | | 6 | [[%ATTACHURL%/Exercise6.pdf][Exercise6.pdf]] | | 7 | [[%ATTACHURL%/Exercise_7.pdf][Exercise7.pdf]] | ---+++ Reviews [[%ATTACHURL%/ResultsReview1.pdf][Results Review1]] [[%ATTACHURL%/ResultsReview2.pdf][Results Review2]] ---++ Requirements for Aktive Teilnahme You have to hand in 75% of all practical assignments. (You have to show reasonable programs and can explain them.) In addition you need to reach 50% of all points of the two reviews. [[OldContent][OLD CONTENT]].
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Topic revision: r32 - 12 Mar 2013,
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