Schulz Lab

AASA 2020 -Advanced Algorithms for Sequence Analysis

General info

• INFO: this is a video lecture with interactive excercises
• Lecture: Videos of the lecture are accessible every Wednesday in the password protected area
• Exercise: biweekly using Zoom with interactive participation. Every second Friday at 1pm, starting from the 13.11.
• You get 6 credit points
• Oral exams at the beginning of semester break, re-exams at the end of the break (exact dates tbd)
• Registration: Please register at the course mailing list if you are interested to join the course, additional information during the course will be announced over the list: register here
• IMPORTANT Introductory Zoom session on the 3rd Nov 2020 6pm with details about the form of the lecture and excercises. Exact connection details will be distributed on the 1st Nov over the mailing list.
• Successful participation in excercises/assignments required to be eligible to take the exam

Course overview

Sequence information is ubiquitous in many application domains. Handling the large amounts of sequence data produced by todays DNA sequencing machines is particularly challenging. 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 transform and the FM index. These algorithms are introduced in the context of modern software packages routinely employed for analysis of large DNA sequencing datasets.