Sequence Analysis 3 (2V + 2Ü)


392105/06 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 Exercises 1
18.04.2024 String matching Exercises 2
25.04.2024 Exact k-mer search (LR) Exercises 3
02.05.2024 Suffix tree construction in linear time Exercises 4
09.05.2024 (Ascension Day)
16.05.2024 Suffix array construction in liner time (LB) Exercises 5
23.05.2024 BWT applications Exercises 6
30.05.2024 (Corpus Christi)
06.06.2024 Number of alignments Exercises 7
13.06.2024 Length-normalized alignment Exercises 8
20.06.2024 Parametric alignment Exercises 9
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)