Proseminar 'Bioinformatics' SS 2012

Type:            Seminar (2 SWS)
Ects:             4.0
Lecturer:      Burkhard Rost
Time:           Monday, 13:30 - 15:00 
Room:          MI 01.09.034
Language:    English

Content

The main aim of a proseminar is to practice scientific talks. Every participant will give a talk in English of about 30 min duration, followed by a discussion of the topic.

Pre-meeting

There were two pre-meetings scheduled

• One meeting on Friday, February 3rd, noon (12:00)(Room 01.09.034 as above) to discuss the general content and the background knowledge of the interested students. 
  Please contact Andrea Schafferhans if you are interested in this seminar, but could not attend this first pre-meeting. 
  Please state your field of study, your semester, your background in biology and biochemistry and why you want to take this seminar (apart from the lack of other options...).
• The second meeting was canceled for lack of students.

Merged!

Since the number of interested students from computer science was very limited, we decided to merge this seminar with the one for bioinformaticians.

Sequence alignment

Dr. Andrea Schafferhans

Finding an alignment of two protein sequences is the basis of all techniques to infer knowledge by homology. This talk shall review well-known sequence alignment methods.

Literature:

• Wikipedia: en.wikipedia.org/wiki/Sequence_alignment
• A.M. Lesk. Bioinformatik: Eine Einführung. Spektrum Akademischer Verlag, 2002.
• A.M. Lesk. Introduction to bioinformatics

Homology modelling

Dr. Andrea Schafferhans

If the structure of a protein has not been resolved experimentally, one can often model the sequence by homology to other sequences. This seminar shall give an overview of homology modelling techniques.

Literature:

• en.wikipedia.org/wiki/Homology_modelling
• A.M. Lesk. Bioinformatik: Eine Einführung. Spektrum Akademischer Verlag, 2002.
• A.M. Lesk. Introduction to bioinformatics

Monte Carlo methods

Dr. Edda Kloppmann

Monte Carlo methods use random sampling for computation. These methods were first used in the 1940s and are still widely applied to obtain predictions for biological systems.

Protein secondary structure prediction

Dipl. Bioinf. Christian Schaefer

Predicting the secondary structure elements comes into play when only the sequence of a protein is known. In this seminar, an overview and discussion shall be given of both historical and more recent approaches.

Literature:

• David Mount, Bioinformatics - Sequence and Genome Analysis (Second Edition), Cold Spring Harbor Laboratory Press