Alignment-free Sequence Analysis with Python Prof. Dr. Sven Rahmann Special Lecture MSc Bioinformatics (and other CS degrees), 4V+2Ü, 9 CP

Hi everyone,

I am sorry to announce that there will be no tutorial today due to a health problem.

In the meantime if you have any questions that we normally discuss during the tutorial session, don't hesitate to write me an email at dang@cs.uni-saarland.de

Have a nice day,
Vu Lam.

Hello everyone,

hope you are enjoying a long weekend with tomorrow's holiday. In the meantime, we have updated the slides on Bloom filters and uploaded the slides on XOR filters, which you can find in the Materials section.

Please remember to complete the practice assignment on computing the FPR of blocked Bloom filters by Friday 02.06. Everything you need (formulas) are on the Bloom filter slides; you just have to put it together and run it for some values of h and c.

To clarify a question that came up: These assignments are, in a sense, optional, i.e. there is no punishment for not doing them. The requirement for passing the course is doing a project (to be discussed on Friday 02.06.) and then passing an exam on the course material and your project. However!, doing these assignments will help your understanding of the material (I hope) and give you some more programming practice before things get busy.

Friday 02.06. is also the day of the next lecture, where we complete the XOR filters (I had planned on completing them last time) and then talk about hashing more generally, e.g., what are good and simple hash functions; what are good collision resolution strategies? I will present project ideas, and you are also welcome to propose your own ideas.

After that lecture there will be a longer break and the following lecture will be on 23.06. During this time between lectures, you should start project work.

Good afternoon,

the slides of today's lecture (and some more) are now online, as well as assignment 3 which asks you to visualize the false positive rate of standard vs. blocked Bloom filters. It is due in 2 weeks (on 02.06.).

As for the updated schedule, the plan is to move ahead with the posted schedule on the main page (except that the 12.05. was moved to 19.05.). This means, the next lecture will already be next week (26.05.) and then one more the week after (02.06.). We will continue a bit on Bloom filters (especially their use as k-mer filters!), and then move to hashing, so we can implement key-value stores for k-mers and associated information.

Good morning,

unfortunately, due to personal reasons, I have to cancel the lecture today. It will be moved to next week. I am really sorry for the inconvenience. The topic is "Bloom Filters", an important basic data structure, with many variations that make it work much better in practice.

An updated schedule will be posted later today.

Sven Rahmann

Hello everyone,

after today's lecture, you are well prepared for a first practice assignment: to write your intbitarray.py implementation, which will allow you to create an array of integers of any bit-width 1 <= w <= 64, without wasting any bits.

Please carefully review the bitarray lecture before you start with the assignment. It is due in 2 weeks from today.

Happy coding!