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Presence in tutorials; preliminary exam datesWritten on 16.04.25 by Sven Rahmann Your presence in the lecture and in one of the tutorials is highly recommended. Formally, presence in the lectures cannot be required, but the subject-specific exam regulations in Bioinformatics actually formally require presence in the tutorials. As the precise regulations differ between study… Read more Your presence in the lecture and in one of the tutorials is highly recommended. Formally, presence in the lectures cannot be required, but the subject-specific exam regulations in Bioinformatics actually formally require presence in the tutorials. As the precise regulations differ between study programs, will not enforce presence. However, we will make the implicit assumptioon that you have regularly attended the lecture and the tutorials when designing the final exam. We also have preliminary dates for the written exam: - Main exam: Monday 28.07., 09-12 (romm TBA) - Re-exam: Monday 29.09., 09-12 (room TBA) |
TutorialsWritten on 14.04.25 (last change on 14.04.25) by Johanna Schmitz Dear all, the weekly tutorials are on Wednesdays, 8:30-10:00 and on Thursdays, 10:15-11:45 in E.2.1, room 007, starting this week. |
Assignment 00Written on 14.04.25 by Jens Zentgraf Dear all, the deadline for assignment 0 is 23:59 today. Assignment 0 is mandatory. Best, |
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Written on 08.04.25 (last change on 08.04.25) by Johanna Schmitz Hi everyone, we created a poll to find the best weekly tutorial slots. You can find the link under Materials. The deadline to fill out the poll is Friday, 11.04. |
Algorithms for Sequence Analysis
(Special lecture 4V+2Ü, 9 CP for MSc Bioinformatics, Advanced lecture to other CS degree programs as well: Computer Science, DSAI, Cybersecurity, etc.)
Note: If you intend to take this course in a later semester, please be aware that the next instance will most likely not be in Summer 2026, but in Winter 2026/27.
Lecture Dates:
- every Tuesday 08:30 - 10:00, starting 08.04.2025
- every Thursday 08:30 - 10:00, ending 17.07.2025
- except on official holidays
- Room: E2.1, room 0.01 (Center for Bioinformatics, seminar room, ground floor)
Tutorials:
- every Wednesday (8:30 - 10:00, E2.1 room 007)
- every Thursday (10:15 - 11:45, E2.1 room 007)
You need to be registered for this course in order to access the Materials section with lecture slides, homework assignments, etc.
Contents
Some of the topics discussed are
- different algorithms for exact pattern search (searching for substrings in longer strings)
- data structures for full-text indexing, in particular suffix tree, array, Burrows-Wheeler transform, FM index
- useful companion data structures: rank (and select) data structures on bit sequences; wavelet trees
- applications of full-text indexes in genomics (repeat finding, etc.)
- error-tolerant pattern search in strings (Hamming distance; edit distance)
- biological sequence alignment and models of evolutionary processes
- algorithm engineering for sequence alignment (affine gap costs; linear space; different objectives)
- the read mapping problem; seed-filter-extend approaches
- text compression algorithms
- alignment-free sequence analysis: basics, methods, successes, challenges
Requirements
The are no special requirements for the course. However, you should be familiar with elementary algorithms and data structures (sorting; stacks, queues) and algorithm analysis (asymptotic notation like O(n)). For bioinformatics, this is a fairly theoretical and formal course about algorithms. For theoretical computer scientists, this is a fairly practical course, actually considering good implementations of different algorithms. Programming skills are absolutely necessary to solve the practical homework exercises. Do not take this course if you have no or poor programming skills; it will not work out well.
Passing the Course
In order to pass this (graded) course for 9 ECTS credits, a number of conditions needs to be satisfied:
- You need to register for the course here in the CMS to access the course materials, including homework.
- You need to achieve at least 50% of all possible points in the homework, in both the theoretical exercises and in the programming exercises (of which there are some, but fewer than theoretical exercises). (Yes, this means at least 50% in each category separately. If you cannot program, do not take this course!)
- You need to attend a tutorial regularly and present some of your homework solutions. The tutors will keep track of when you do this.
- When you qualify for the exam, you need to register for it in the LSF system (instructions will come towards the end of the semester; exam dates will be shortly after the lecture period). LSF registration closes one week before the exam; no exceptions.
- The exam will check your understanding of a broad variety of topics taught in the course and from the homework. Usually the exam is an oral exam; it will only be a written exam if the number of qualifying course participants is 15 or above. This will be estimated and announced within the month of April.
No Grade Improvement
Important: Once you have passed the exam, you cannot re-take it to improve your grade. This is different from basic lectures where there is an improvement possibility within the same exam period.
No Automatic Re-Admission for the Next Exam Period
If you qualified for the exam in one exam period (say, summer '24), but then failed the exam(s), and you want to re-take the exam one year later (say, summer '25), then you have to re-qualify (i.e., do the homework again and obtain enough points). In any case, it is highly recommended to prepare for the exam by solving the homework assignments!