Algorithms for Sequence Analysis

Algorithms for Sequence Analysis - Tobias Marschall & Marcel Schulz

General info

  • Spezialvorlesung (2+1) with exercises
  • Lecture : Wednesday 10:15-11:45, room 001, Campus E1.7 (MMCI)
  • Exercise: Wednesday 8:30-10:00, room 001, Campus E1.7 Exercise is held biweekly starting 6th of May
  • You get 5 credit points
  • Master students are eligible
  • Oral exams: 09.09.2015 and 10.09.2015
  • Oral re-exams: 16.10.2015
  • 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

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.

Course material

Course material will be available here: password protected area.


We will mostly make use of the following books during the lecture:
Enno Ohlebusch - Bioinformatics Algorithms (more details on the book are available here )
Gonzalo Navarro & Mathieu Raffinot - Flexible Pattern Matching in Strings