Algorithms for Sequence Analysis

Dear all,
a quick reminder how you qualify for the final exam.
You need:
- 50% of theory points,
- 50% of the programming points,
- present 2 solutions in the tutorial.
Many have only presented once or not at all. 
There are only 2 tutorials left before the exam. In these, we will discuss assignment 9 (04.07.2024) and assignment 10 (18.07.2024). Please join the tutorials and present your solutions. 
We can also discuss multiple solutions for the same task.

We have created a small web app you can use to prepare for the exam. You can find it here:
https://gitlab.com/rahmannlab/alsa-app

It covers a large part of the topics and allows you to work on the topics with different inputs and compare them with a solution.

The written exam for Algorithms for Sequence Analysis takes place on Wednesday 31.07.2024, 10:00 - 13:00.

The re-exam (no grade improvement possible if the first exam was passed!) takes place on  Friday 11.10., 09:00 - 12:00.

We currently think that the exams will be written in the CBI room 0.07, but this might change.

Dear all,

as Thursday (30.05.) is a holiday, there will be no tutorial. 
Please come to the tutorial on Wednesday (29.05).
This will be the last Wednesday tutorial, as at most one person attended the last few weeks.

Assignment 06 is due in *2 weeks*. This means that the next tutorial (after this Wednesday) will be on Thursday 13.06.

It has come to our attention that some of you have tried to copy solutions. This is plagiarism. (Solutions were actually wrong, too.) Plagiarism will be punished to the maximum extent. It is unethical and has no place in academia. This is what will happen:

1. You will be kicked out of the course.

2. You will be reported to the examination board.

3. In case of a repeated report to the examination board, they can remove you from the study program.

This is not a joke.  Before you think of copying (from someone else, from the internet, from ChatGPT, wherever), think again. If you find the assignments hard, come to the tutorials where the tutor can explain things. If you don't have enough time, don't take the course. Copying is not a solution, it's a problem, and if you do it, it can destroy your academic career entirely.

 

Dear all,

there was an error on task 4 in assignment 01. 

If you use more than one character, you cannot skip the last characters in the pattern. 
For P=BAAAAB and l=2 we would skip AB and if we see AB in the text we would do a shift of the pattern length 6.

BAAAAB
BAAAABAAAABAAA    shift based on AB 

      BAAAAB
BAAAABAAAABAAA    We miss the second hit.

To deal with this, you have to check if a part of the suffix (of length l) of the pattern is a prefix of the pattern. (Does the end overlap the start of the pattern). Then you have to adapt the shift for all suffixes for which this is the case.

I uploaded a new assignment in which you can find the shifts for P=BAAAAB for l=1,2,3.

If you have questions, do not hesitate to ask in the forum.

Best 
Jens
 

Dear all,

the deadline for assignment 00 is approaching (today 22.04. 23:59).
Please make sure that you upload your solution to the cms.

If you solve the task in python, please upload the python file.
If you solve the assignment in another language, please upload all necessary files and provide a short explanation how to (compile and) execute the code.

Best
Jens