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Sequence Analysis and Phylogenetics (2VL)

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

PDF (3.6 MB, 2017-04-06)
PDF (optimized version, 2.3 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 algorithmical details have been shortened. But these lecture notes might be helpful to clarify and deepen many of the important topics.

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

Lecturing:
Depending on the situation with the virus, the lecture will be held in-class (as usual), or remote. In the latter case, the video recordings will be posted via moodle, while the slides, other material and administrative messages can be found in KUSSS. Urgent messages (like cancellations or room changes in the last moment) will be communicated via email to all registered students.

The lecture will be held “remote”, not in-class. The units will be recorded on video and posted via moodle, while the slides, other material and administrative messages can be found in KUSSS. Urgent messages will be communicated via email to all registered students.

If there are video recordings, they will be kept online until the end of next summer semester.

Exams
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 in order 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 2021). 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.

In contrast to the lecture, all exams are planned for in-class. Due to the virus and the distance regulations, we probably have to split the exams into two that are held on the same day and assign each student to one of those. But beware: this regulation could be changed, depending on the number of students doing the exam, and depending on the situation with the virus at that time.

Content:
Other than an introductory lecture, we will have six 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

 

Exercises (365.062)

The exercises will be held irregularly and mostly on a two-weekly basis, but always on the scheduled time (Fridays, 12:00-13:30). As with the lectures, they are remote, not in-class. Again, the videos are kept online. I will ask you to send me emails one or two days before each class with questions or things that I should clarify from the lecture and I will try to answer those from the classroom.

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 (exactly like in previous years). The sum of the points will determine the mark that you get.

 

Introductory lecture (for both VL and UE)

A video with some more details about the lecture, including exercises, will be posted during the first days of October.