- Omer Alkhnbashi

The aim of the practical course is to acquire and implement a manageable amount of algorithms
out of a sub-branch of bioinformatics. Based on a literature search for each algorithm, a comprehensive description
and implementation using Python will be the aim of the course.

Therefore, the programs should be implemented, such that command-line calls and the usability as modules is realized.

Within one session, the (almost) finished program-codes will be cross-validated and evaluated by the courses' participants.

English is the course language -> Presentations, Documentations and the Comments within the code have to be in english!

- Literature Search
- Description of the Algorithms (in LaTeX-Format)
- well documented source code (Python)
- Input-failure robust parameter parsing

- 23.Oct 2017 Introduction / Overview and Distribution of Topics
- 13.Nov.2017 Presentations (10-20 min)
- 20.Nov.2017 Introduction to the project (implement the algorithms using Python)
- 22.Dec.2017 Hand-in of the preliminary version of the report and code "Sequence Alignment"
- 29.Jan.2018 Hand-in of the preliminary version of the report and code "Multiple Alignment and Basic Structure prediction"
- 05.Feb.2018 Cross-Validation Day
- 12.Feb.2018 Final Submission of Code and the report

- Needleman-Wunsch-Algorithm
- Gotoh-Algorithm

- Needleman-Wunsch - Algorithm for n = 3 sequences

- Sum-of-Pairs-Algorithm
- Feng-Doolittle-Algorithm
- UPGMA / WPGM (Unweighted / Weighted Pair Group Method using Arithmetic mean)

- Nussinov-Algorithm

- Background about the topics / algorithms / modules (Wherefor? Why? For which reason?)
- Prepare a coarse overview to
*each*Algorithm. (What is special? Where is the advantage? ...) - Focus on:
*"I basically understand, how it works!"* - Prepare the mini-talks, even if you have problems in understanding - we will discuss them together!
*Maximum*10 mins per algorithm! Keep it short!

- Introduction to python:Interfaces and materials for the programming course
- Tasks and Implementation guideline
- Introduction Slides
- A (not so) short introduction to LaTeX : (english) or (german)
- LaTeX Templates for the Documentation: german (tex) and english (tex)
- Substitution Matrices for Alignments: PAM250 und Blosum62

- Peter Clote and Rolf Backofen.
**Computational Molecular Biology: An Introduction.**Jon Wiley & Sons, Chichester, August 2000. - Richard Durbin, Sean Eddy, Anders Krogh and Graeme Mitchison.
**Biological sequence analysis - Probabilistic models of proteins and nucleic acids.**Cambridge University Press, Cambridge, 1998. - Dan Gusfield.
**Algorithms on Strings, Trees, and Sequences.**Cambridge University Press, Cambridge, 1997.