Lecture Bioinformatik I
Lecturers
Lecture: Rolf Backofen, Florian Eggenhofer, Dilmurat Yusuf, Omer Alkhnbashi
Exercise: Rick Gelhausen, Stefan Mautner, Teresa Müller
Dates
- Lecture:
Wed 10-12, via Zoom (instructions for installation can be found here)
- Exercise Session:
Fri 10-12
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:
- Lecture recordings: Due to the current situation, lecture
recordings will be provided.
- 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, e.g. by annotating printed versions of the slides.
- 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.
Forum
- We set up a forum in ILIAS to enable exchange with of your fellow students.
Schedule and Material
- [04.11.2020] Introduction, Organization, Overview
- Kickoff lecture (via Zoom) at 10am
- Slides:
- Recordings:
- Implementation Tasks:
- Further Reading:
- [06.11.2020] NO exercise session !
- [11.11.2020] Essential Biology Basics
- Slides:
- Recordings:
- Exercise sheet:
- Implementation Tasks:
- Further Reading:
- [13.11.2020] NO exercise session !
- [18.11.2020] Edit Distance, Alignment Distance, Pairwise Sequence Alignment
- Q and A session for Essential Biology Basics:
Add questions concerning the previous lecture here until 15.11.2020 - 15:00,
they will be covered in Zoom at 10 am with the following credidentials:
https://uni-freiburg.zoom.us/j/87303575896
Meeting ID: 873 0357 5896
Passcode: 4S*mn3A2.
- Slides:
- Recordings:
- Exercise sheet:
- Implementation Tasks:
- [20.11.2020] Exercise session: Essential Biology Basics. Write down your questions until 19.11.2020 at 14:00
Questions will be answered in the Zoom session at 10:15 with the following login credidentials:
https://uni-freiburg.zoom.us/j/88511636209
Meeting ID: 885 1163 6209
Passcode: z0WGAFT5@
- [25.11.2020] Global Pairwise Sequence Alignment
- Q and A session for Edit Distance, Alignment Distance, Pairwise Sequence Alignment:
Add questions concerning the previous lecture here until 22.11.2020 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Literature:
- Exercise Sheet:
- Implementation Tasks:
- [27.11.2020] Exercise session
Questions will be answered in the Zoom session at 10:15 with the following login credidentials:
https://uni-freiburg.zoom.us/j/88511636209
Meeting ID: 885 1163 6209
Passcode: z0WGAFT5@
- [02.12.2020] Non-linear Gap Scoring
- Q and A session for Global Pairwise Sequence Alignment:
Add questions concerning the previous lecture here until 29.11.2020 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Literature:
- Implementation Tasks:
- Exercise Sheet:
- [04.12.2020] Exercise
-
Questions will be answered in the Zoom session at 10:15 with the following login credidentials:
https://uni-freiburg.zoom.us/j/88511636209
Meeting ID: 885 1163 6209
Passcode: z0WGAFT5@
- [09.12.2020] Local Pairwise Sequence Alignment
- Q and A session for Non-linear Gap Scoring:
Add questions concerning the previous lecture here until 06.12.2020 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Literature:
- Implementation Tasks:
- Exercise Sheet:
- [11.12.2020] Exercise
-
Questions will be answered in the Zoom session at 10:15 with the following login credidentials:
https://uni-freiburg.zoom.us/j/88511636209
Meeting ID: 885 1163 6209
Passcode: z0WGAFT5@
- [16.12.2020] Bio Introduction Proteins
- Q and A session for Local Pairwise Sequence Alignment:
Add questions concerning the previous lecture here until 13.12.2020 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Implementation Tasks:
- Exercise Sheet:
- Literature:
- [18.12.2020] Exercise
- [13.01.2021] Markov chains
- Q and A session for Bio Introduction Proteins:
Add questions concerning the previous lecture here until 10.01.2021 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Implementation Tasks:
check and understand this
Markov-chain-based text generator
- Sheet 7
- write your questions here until 21.1. 2pm
- when you have solved the sheet you can compare your solution with sheet 7 solution
- [15.01.2021] Exercise
- [20.01.2021] Substitution Scoring
- Q and A session for Markov chains:
Add questions concerning the previous lecture here until 17.01.2021 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Literature:
- Implementation Tasks:
recompute the PAM250 matrix for amino acids using the following information from
(Dayhoff et al., 1978)
- [22.01.2021] Exercise
-
Questions will be answered in the Zoom session at 10:15 with the following login credidentials:
No Questions were asked.
- [27.01.2021] Multiple Sequence Alignment and Summary
- Q and A session for Markov chains:
Add questions concerning the previous lecture here until 24.01.2021 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Literature:
- Implementation Tasks:
- [29.01.2021] Exercise
- Sheet 9
- seq.fa
- when you have solved the sheet you can compare your solution with sheet 9 solution
-
Questions will be answered in the Zoom session at 10:30 with the following login credidentials:
https://uni-freiburg.zoom.us/j/88511636209
Meeting ID: 885 1163 6209
Passcode: z0WGAFT5@
- [03.02.2021] Phylogeny Reconstruction + UPGMA
- Q and A session for Multiple Sequence Alignments:
Add questions concerning the previous lecture here until 31.01.2021 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Literature:
- Implementation Tasks:
- [05.02.2021] Exercise
- [10.02.2021] Maximum Likelihood Trees
- Q and A session for Phylogeny Reconstruction + UPGMA:
Add questions concerning the previous lecture here until 07.02.2021 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- Slides:
- Recordings:
- Literature:
- Exercise:
- [12.02.2020] Quartet tree puzzling
- slides:
- Recordings:
- Literature:
- implementation tasks:
- Exercise:
- [17.02.2020] - Q and A session for Maximum Likelihood Trees + Quartet tree puzzling:
Add questions concerning the previous lecture here until 14.02.2021 - 15:00,
they will be covered in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- [24.02.2020 - 10:15am] optional question session
- Join us in Zoom at 10:15 am with the following credidentials:
https://uni-freiburg.zoom.us/j/89257303943
Meeting ID: 892 5730 3943
Passcode: ^rd62b8Z8
- [16.03.2020] 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