Lecture Bioinformatik I
Lecturers
Lecture: Rolf Backofen, Martin Raden, Dilmurat Yusuf, Florian Eggenhofer
Exercise: Florian Heyl, Teresa Müller, Rick Gelhausen
Dates
- Lecture:
Wed 10-12, building 106 - SR 00 007 (MMR)
- Exercise:
Fri 10-12
- Exercise class 1 - SR 00 007, Build. 106
- Exercise class 2 - SR 02 017, Build. 052
- Exercise class 3 - SR 00 006, Build. 051
- Examination will be a written test so far scheduledfor 11.03.2020 at 1pm in HS 00 006
(for final date + time check HISinOne)
- Evaluation of WS 2019 : [pdf]
Topic and Objectives
This is an introductory lecture to bioinformatics and is mandatory for the group's
advanced lectures in bioinformatics.
The topics of the course include sequence alignment and comparison,
Markov Chain models, and building phylogenetic trees.
Objectives: The course shall give an overview of basic bioinformatics
topics and understanding of some fundamental algorithms. The special focus
of the course is on sequence analysis.
Requirements
- basic knowledge about molecular biology
- basic understanding of algorithms
Although the course requires a basic understanding of molecular biology, an introduction
to the necessary foundations is also given in the respective lectures.
Enrolled students agree to ...
When you enroll for this course, you agree to the following general set-up:
- No lecture recordings: We will not record any lecture
of this course. There are multiple reasons: We are investing time to
give the course and expect any registered student to do the same, ie. to
join the presentation and discussion.
Why? We believe that actively taking part in a lecture, taking
notes and asking questions, trains key skills required in future job
situations such as listening and quick comprehension of difficult content.
- If you miss a session, you are supposed to contact your fellow
students to get informed. If you still have questions, please write
them in detail to us via email.
- Lecture slides are not sufficient to understand or
learn a topic. They are not intended as a reader but as additional material
to avoid typos on the blackboard and to present examples etc.
Thus, you are supposed to take your own notes of the discussed
lecture material, eg. by annotating printed versions of the slides.
- If you have a question or lost track during the lecture, raise a
hand and let us know! The idea is that you understand (most of)
the topics on site! Final details and further examples are part of the
exercises. Furthermore, we provide links to respective original literature
and text books for each lecture separately.
- Solving exercise sheets is optional but highly recommended.
Observations from previous
semesters show that attending the exercises and solving the sheets
deepens your understanding.
We will provide solution sheets that might only show the final result
but not each calculation step.
You can use the exercise session for (supervised) solving the sheets or
to ask questions. You can solve them independently or as group.
We do not grade nor collect exercises.
- Given that you gain 6 ECTS, your workload is estimated with up to 8h
per week dedicated to this lecture. Thus, there is plenty of time for
reading additional material, rechecking of previous lecture material,
implementation of algorithms.
For the latter, we point to respective programming problems on
Rosalind.
In our experience, it is highly beneficial to solve these implementation
tasks for a thorough understanding.
Rosalind implementation tasks
- We have setup a class within Rosalind that lists problems related
to the course's material with respective due dates, typically the next
lecture session.
- In order to access the Rosalind class you have to follow the Rosalind class enroll link.
- Your solution submission has to be accompanied with the respective source code.
Once you have successfully solved a problem, you can post your source code within a respective forum to discuss and review the source submissions of your fellow students.
Schedule and Material
- [23.10.2019] introduction, organization, overview
- slides:
- implementation tasks:
- further reading:
- [25.10.2019] NO exercise session !
- [30.10.2019] essential biology basics
- slides:
- implementation tasks:
- further reading:
- [01.11.2019] Sheet 1 will be discussed on [08.11.2019]
- [06.11.2019] edit distance, alignment distance, pairwise sequence alignment
- slides:
- implementation tasks:
- [08.11.2019] exercise
- [13.11.2019] global pairwise sequence alignment
- slides:
- literature:
- implementation tasks:
- [15.11.2019] exercise
- [20.11.2019] non-linear gap scoring
- slides:
- literature:
- implementation tasks:
- [22.11.2019] exercise
- [27.11.2019] local pairwise sequence alignment
- slides:
- literature:
- implementation tasks:
- [29.11.2019] exercise
- [04.12.2019] bio introduction proteins
- slides:
- implementation tasks:
- literature:
- [06.12.2019] exercise
- [11.12.2019] Markov chains
- [13.12.2019] exercise
- [18.12.2019] substitution scoring
- slides:
- literature:
- implementation tasks:
recompute the PAM250 matrix for amino acids using the following information from
(Dayhoff et al., 1978)
- [20.12.2019] exercise
- [08.01.2020] multiple sequence alignment and summary
- slides:
- literature:
- implementation tasks:
- [10.01.2020] exercise
- [15.01.2020] phylogeny reconstruction + UPGMA
- slides:
- literature:
- implementation tasks:
- [17.01.2020] exercise
- [22.01.2020] maximum likelihood trees
- [24.01.2020] exercise
- [29.01.2020] quartet tree puzzling
- slides:
- literature:
- implementation tasks:
- [31.01.2020] - no exercise session
- [05.02.2020] - no lecture session
- [07.02.2020] - exercise
- [12.02.2020 - 10am] optional question session
- send your open questions till 11.02.2020 via email to Martin
- [11.03.2020] written examinations
Algorithm implementations
We observe that the deepest understanding of the course content is gained by
implementing the introduced algorithms. In order to cross-check the
results of personal implementations and to enable a fast example
generation and study, we offer Javascript-based implementations and
visualizations for most of the algorithms via the
Freiburg RNA tools - Teaching
webserver.
Books
-
Computational Molecular Biology: An Introduction.
Peter Clote and Rolf Backofen.
Jon Wiley & Sons, Chichester, August 2000.
-
Biological sequence analysis - Probabilistic models of proteins and nucleic acids.
Richard Durbin, Sean Eddy, Anders Krogh and Graeme Mitchison.
Cambridge University Press, Cambridge, 1998.
-
Algorithms on Strings, Trees, and Sequences.
Dan Gusfield.
Cambridge University Press, Cambridge, 1997.
-
Bioinformatik Interaktiv.
Grundlagen, Algorithmen, Anwendungen.
Rainer Merkl und Stephan Waack.
WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim 2009.
Substitution matrices