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Sequence Analysis and Phylogenetics (2VL + 2UE)

Video Streaming

Since attendance is not strictly required in SA, you could learn for SA only from the slides and the videos in moodle, but this is NOT RECOMMENDED. People from previous years who did that, had „limited success“, to put it mildly, in the exams. For SA-UE, attendance is mandatory.


Sequence Analysis and Phylogenetics (2VL), “SA”, 365.060

Lecture Notes:
There are NO lecture notes, but a version from a former lecture can be downloaded here.

PDF, opens an external URL in a new window, opens an external URL in a new window (3.6 MB, 2017-04-06)

Note that the content is quite different from the current lecture. Some new topics have been introduced, some others dropped, and many algorithmic details have been shortened. But these lecture notes might be helpful to clarify and deepen many of the important topics.

All slides used in class will be posted in KUSSS, shortly after each lecture.

Currently, we plan for normal in-class lectures, but a new Covid outbreak could change that. Stay tuned!

Slides, other material, and administrative messages can be found in moodle, especially in the “News” forum on top of the course page. Urgent messages (like cancellations or room changes in the last moment) will be communicated via email to all registered students.

There will be two exams during the semester, one in November or December, the other one at the end of January. Each of these exams will cover roughly half of the lecture, there will be no overlap. The total grade will depend on the sum of points achieved in both exams. You will have to attend both exams to get graded. In other words, we split the usual final exam up into two.

You will have a second opportunity at the beginning of the next semester (March 2022). This exam will not be split, it covers the whole lecture. Note that if you do only one of the two original exams, then those points are actually lost.

All exams are planned for in-class, like the lecture itself. But again, the Covid situation will influence the organizational setting.

Other than an introductory lecture, we will have seven main topics in this lecture

Basics and Resources Quick overview about the biological background
The interest in sequences? What tools are out there?
Similarity and Scoring What does it mean if two sequences are called „similar“?
How do you assess the level of similarity?
Pairwise alignment How do you align two sequences in an optimal way?
Multiple alignment Extending the concept of pairwise alignment to n>2 sequences
Phylogeny Deriving evolutionary relationships from the result of a multiple sequence alignment
Beyond alignment Other methods to assess sequence similarity
Sequence models Applications of machine learning models to biological sequences

The first six topics are held by Alois Regl, while the last one will be presented by Günter Klambauer.
In addition, we plan for an external lecturer covering sequence comparisons on a genome-wide scale.


Exercises in Sequence Analysis and Phylogenetics (2UE), “SA-UE”, 365.062 and 365.265

Due to the large number of students, the exercises will be split into two groups. How the splitting is organized, is still to be developed.
The exercises will be held irregularly and mostly on a two-weekly basis, but always on the scheduled time (Thursdays, 15:30-17:00 and 17:15-18:45). It will not be possible to switch during the semester.

Grading for the exercises is independent of the lecture. You will get assignments with a due date, you hand in your solutions via email and these will be evaluated. The sum of the points will determine the mark that you get. The exercises are held by Florian Sestak, grading will be done by two tutors, Thomas Tschoellitsch and Amon Tesla.


Introductory lecture (for both VL and UE)

An introductory lecture, covering all the organizational details for both SA and SA-UE, will be held on October 10 (Monday), 12:00 – 13:30 in HS 6, with streaming to Vienna and Bregenz.