AdvancedAlgorithms12 < ABI

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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]].