====== Sequence Analysis 3 (2V + 2Ü) ======
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| [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=449953590|392105]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=449967587|06]] | Stoye, Robidou | Summer 2024 | Thu 10:00-11:30/11:30-13:00, U10-146 |

===== Content =====
Sequence analysis is more than bioinformatics.
Here we will discuss some advanced sequence analysis topics that go beyond the introductory classes Sequence Analysis 1 and Sequence Analysis 2 (formerly "Sequenzanalyse") which are mostly concentrating on bioinformatics applications.
The topics in detail are flexible, probably some automata-based methods will be covered, modern index data structures and compression, and also some classical methods. Some might be more relevant for bioinformatics applications, some less.

===== Literature =====
Pointers to the original literature will be given during the class.

===== Exercises =====
Solutions to exercises may be presented to the teacher at the beginning of the exercise class.

===== Exams =====
Oral exams will be offered on an individual basis during the summer 2024. Please contact the teacher.

===== Topics =====
| **Date** | **Topic** | **Exercises** |
| 11.04.2024 | Basics | {{teaching:2024summer:sa3:exercises01Basics.pdf | Exercises 1}} |
| 18.04.2024 | String matching | {{teaching:2024summer:sa3:exercises02StringMatching.pdf | Exercises 2}} |
| 25.04.2024 | Exact //k//-mer search (LR) | {{teaching:2024summer:sa3:exercises03kmers.pdf | Exercises 3}} |
| 02.05.2024 | Suffix tree construction in linear time | {{teaching:2024summer:sa3:exercises04SuffixTreeConstruction.pdf | Exercises 4}} |
| 09.05.2024 | (Ascension Day) | -- |
| 16.05.2024 | Suffix array construction in liner time (LB) | |
| 23.05.2024 | BWT applications | |
| 30.05.2024 | (Corpus Christi) | -- |
| 06.06.2024 | Number of alignments | |
| 13.06.2024 | Length-normalized alignment | |
| 20.06.2024 | Parametric alignment | |
| 27.06.2024 | How many squares can/must a string contain? | |
| 04.07.2024 | Finding and representing all tandem repeats in a string | |
| 11.07.2024 | ??? (LR) | |
| 18.07.2024 | ??? (LR) | |