Algorithms for Sequence Analysis

Thema

Sequence information is ubiquitous in many application domains. DNA sequencing data are one example that motivates this lecture, but the focus of this course is on algorithms and concepts that are not specific to bioinformatics. This lecture addresses classic as well as recent advanced algorithms for the analysis of large sequence databases. Topics include: full text search without index; approximate pattern matching; index structures such as suffix trees and suffix arrays, Burrows-Wheeler transformand the FM index; data compression; multiple sequence alignment; and min hashing.

Allgemein

Assistent und Übungsleiter: Fawaz Dabbaghie

Vorkenntnisse: Bioinformatics I+II oder vergleichbare Veranstaltungen, Grundkenntnisse in Python

• Erfolgreiches Bearbeiten der Übungen
• 50% Theoriepunkte
• 50% Praxispunkte
• Bestehen der Klausur

Termine

Vorlesungsbeginn: 05.05.2020

Vorlesungstermin: Di. 12 Uhr, Zoom

Fragestunde: TBD

Übungstermin: TBD

Hauptklausur: First week of August 2020. (Room TBA)

Nachklausur: TBD

Materialien

You can find an introduction to Python3 and its data structures here.

Lecture time: Tuesdays, meeting open at 12:00, questions can start at 12:15 for students who come a bit later. Zoom meeting link

Tutorial zoom meeting link here. Backup link if we take more than 45 minutes here.

Tutorials will be bi-weekly on Wednesday at 3 pm CET. First tutoria is going to be on the 13th of May at 3 pm CET.

For questions and registration, email: Fawaz.Dabbaghie@helmholtz-hips.de

You can find some very useful lecture notes here.

Lecture material:

• lecture 1: part 1 here, part 2 here, slides here.
• Lecture 2: part 1 here, part 2 here, part 3 here, slides here.
• Lecture 3: part 1 here, part 2 here, part 3 here, slides here.
• Lecture 4: part 1 here, part2 here, slides here.
• Lecture 5: part1 here, part2 here, part3 here, slides here.
• Lecture 6: part1 here, part2 here, part3 here, slides here.
• Lecture 7: video here, slides here.
• Lecture 8: part 1 here, part 2 here, part 3 here, slides here.
• Lecture 9: part 1 here, part 2 here, part 3 here, slides here.
• Lecture 10: part 1 here, part 2 here, slide here.

Assignments:

• Assignment 1 here.
• Assignment 2 here.
• Assignment 3 here.
• Assignment 4 here.