Algorithms for Sequence Analysis

Dear all,

please evaluate the "Algorithms for Sequence Analysis" course (separately for lecture and tutorial). The links are on top of the Materials section. Unfortunately, they are only valid until SUNDAY, so please evaluate us this week! Thank you for your time; especially your free-text feedback helps us to improve the course.

On another note, we have put the last regular assignment (#11) online.

There will be an optional bonus assignment (#12) next week that you can use to get a small number of missing points if necessary. (In general, bonus means: The points you receive will be counted towards your total, but the maximum possible points of these tasks are not counted for the requirements.)

Dear all,

the first exam dates for "Algorithms for Sequence Analysis" are 

- Friday 28.07.2023
- Monday 31.07.2023
- one more day (either Thursday 27.07., or Tuesday 01.08.): Can those who cannot make it on the Friday or Monday please indicate to me (rahmann@cs) whether Thursday 27.07 or Tuesday 01.08. is better?

The second round (re-exams) will be later in October (week of 9-13); the number of days will depend on the number of re-exams. 

Dear all,

some information regarding the tutorials of the next weeks.

- 06.06. and 08.06 no tutorials. 

- 15.06: No tutorial, please join the tutorial on Tuesday (13.06).

Programming task assignment 06:

It seems that there was a bit of confusion regarding the programming task of assignment 06. The deadline as stated on the assignment was yesterday (01.06) at 23:59. I extend the deadline until today (02.06.) 23:59. So, please submit your solutions today.

Jens

Hello everyone,

a few updates about the next lectures:

- No lectures next week (I am away on Tuesday, and Thursday is a holiday).

- The next lecture is thus on Tue 13.06., about compression (bzip2 using the BWT, but also other compression methods).

- This will end the (big) chapter 2 on text indexing. We will then move on to chapter 3 on error-tolerant pattern search.

And about today's assignment 07:

- The assignment is due in 2 weeks (15.06.), but contains roughly work for 1 week.

- It will be uploaded this afternoon.

Have a nice week!

Hello everyone,

as it was asked about several times: The final exam will be an oral exam about the lecture + exercises, but you won't have to do programming during the exam (however, you need to have understood your programming exercises, i.e. you do not need to write code, but may need to read code).

One of you was so kind to create a doodle about the most convenient exam dates in the first two weeks in the lecture-free period. Thank you. The link is in the forum; please vote! I will select the two best consecutive dates on which I am also available.

A re-exam (for all who cannot make it to the first exam or fail) will be conducted towards the end of the lecture-free period, shortly before the start of the winter semester lectures. These dates will be discussed later.

Good evening,

we would like to give you heads up on the next few lectures, as the schedule will be slightly irregular.

Tomorrow (Thu May 11) is a regular lecture, and we will start discussing a linear-time suffix array construction algorithm (SAIS). Probably we will only discuss the easy part of the algorithm. We will also put out assignment 05 tomorrow, which is longer than usual and will last for 2 weeks. It contains one assignment (05.3) on O-notation and one assignment (05.4) on amortized analysis to give you some practice with those topics. If you are not very familiar with them, we will put some links into the Materials/Resources where you can find helpful videos about them. Then, the exercises are just logical thinking and common sense.

The reason for the long assignment is that there will be a break in the lecture schedule, as I am away next Tuesday, and Thursday is a holiday (Ascension day / Father's day). So, no lectures next week! Also, no exercises, and your questions about assignment 05 should go to the forum if possible.

On the Tuesday after next week, we will conclude our discussion of the SAIS algorithm and then explore further extensions of suffix arrays and related things.

Dear all,

this morning, we have (already!) completed chapter 1 of the course (exact online pattern search algorithms). The slides are in the Materials section now. As always, we appreciate feedback when you find errors or omissions. Next week, we will begin the next chapter about index data structures.

Please remember to submit assignment 2 by tonight. Later today, we will upload assignment 3, which will be due in 1 week.

Hello everyone,

the first week is already over, and in the first lecture on Thursday, we discussed administrative business, basic definitions, the exact pattern search (or pattern matching) problem, and analysed the naive algorithm, both in a worst-case and in an average-case sense, with perhaps an unexpected result. Over the next week, we will discuss various better algorithmic approaches than the naive one.

A first assignment sheet has been uploaded; it is due on Thursday (20.04.)! Please indicate your tutorial preferences as soon as possible; we want to make the tutorial assignment on Monday, so you can go to your assigned tutorial on Tuesday or Thursday if you have any questions next week.

In the meantime, questions can be asked in our forum.

We have also posted a link to the 2022 lecture videos in the Materials; perhaps in can be helpful. However, the 2023 exam will be about the 2023 lectures, and small content differences will occur, especially towards the end of the term!