Algorithms in Bioinformatics

BIOINF4110 Sequence Bioinformatics

LecturerProf. Dr. Daniel Huson and Anupam Gautam
Time and place

Mondays, 10:15-12:00, Wednesdays 10:15-12h. (Venue: F119, Sand 6/7)

Lectures will be held in person and also recorded and uploaded to Ilias.

RegisterVia Ilias.
AssignmentsWill be made available on Wednesdays and are due 7 days later on Wednesday, 10 a.m.
TutorialsMondays, Wednesdays, Thursdays 8:15-10:00
ExamThe exam will take place in two parts. Part 1: Dec 4th 2024, Part 2: Feb 5th 2025
AudienceMaster students: Bioinformatics, Medical Informatics, Computer Science
LanguageEnglish
LinksAlma Ilias

Contents

Sequence Bioinformatics focuses on concepts, data-structures and algorithms for sequence analysis. Our goal is to teach you to understand, to be able to implement and to apply the most important algorithms used in bioinformatics. Programming assignments are to be solved in Java. Students will be assigned projects in which the goal will be to address a biological problem using methods discussed in the lectures.

Some contents of this lecture were already taught in "Grundlagen der Bioinformatik". While we try avoid overlap with that bachelor level course, some content is so fundamental that we cannot completely avoid some repetition of earlier material. This is for the benefit of students that do not have a BSc in bioinformatics. 

Script and assignments

The script and assignment sheets will be made available via Ilias. Also, please upload your solutions to the assignment sheets there.

Schedule

The following schedule is subject to change. 

DateTopicAssignments
14.10.1. Introduction 
16.10.2. Pairwise sequence alignment (global, local, overlap, linear and affine gaps, linear space and banded)Ass. 01
21.10.continued 
23.10.3. Multiple alignment (progressive, using ILP)Ass. 02
28.10. AG4. DIAMOND protein alignment 
30.10. AG5. Pan genome analysisAss. 03
04.11.3. continued 
06.11.6. Phylogenetics (distance-based, max parsimony, max likelihood, Bayesian analysis)Ass. 04
11.11.continued 
13.11.continuedAss. 05
18.11. AG7. Microbiome analysis (16S, WGS) 
20.11. AGcontinuedAss. 06
25.11.6. continued 
27.11.8. Suffix trees (MUMs, inexact matching, maximal repeats)Practice exam
02.12.continued 

04.12.24 11-13h

N06, Morgenstelle

Exam part I This will cover the first part of the course, chapters 2-7.

 

Ass. 07
09.12.8. continued 
11.12.9. Genome comparison (Mauve and mash)Ass. 08
16.12.continued 
18.12.10. Read mapping (Bowtie and minimap)Ass. 09
 Christmas break 
08.01.25 continuedAss. 10
13.01.2512. Sequence assembly (Velvet and miniasm) 
15.01.25continuedAss. 11
20.01.2513. Population genetics 
22.01.25continuedAss. 12
27.01.25 in A301, Sand14. SVMs 

29.01.25 

8:15-10:00 C118a, Sand

10:15-12h, F119, Sand

Group project presentationsPractice exam
03.02.25  Exam prep. 

05.02.25 12-14h

N10+11, Morgenstelle

Exam part II This will cover the second half of the course, chapters 8-14.

 

 
   
Makeup exam

Thursday, April 3rd, Part 1: 8-10h, Part 2: 10-12h,

Date and location: F119 Sand 6/7

 

How to get credit for this course

  • Always participate in the weekly problem sessions and actively present your results. If you miss more than two tutorials, then you will not be allowed to take the exam.
  • Assignments are set weekly and are due the following week.
  • Obtain at least 50% of all points. If you obtain 70%, 80% or 90% of all possible assignment points, then you will receive bonus points toward your exam.
  • Pass both parts of the exam.