Fortgeschrittene Methoden in der Bioinformatik (10-INF-BIO4)
--> Due to the circumstances, there will be no classroom teaching for this module. We will use an inverted classroom format instead:Below you find reading material on the theoretical background for our project. You are requested to familiarize yourself with the material before consultation/discussion sessions that will (try to) conduct via Leipzig university jitsi instance. (https://meet.sc.uni-leipzig.de/).
jitsi does not require any installations on your computer and should work in any browser. A link to our jitsi sessions will become available here shortly before the sessions.
A short session to test the feasibility, to introduce our project and
to clarify the procedures will be at the orginally planned starting
date
APRIL 01 2020, 11:00-12:00
ARPIL 17 2020, 11:00-12:00
Next consultation Wednesday 29 Apr 2020, 11:30-13:00
https://meet.jit.si/DrivingFinalsMissRecently
- Waehlen sie einen nickname im chat um sich zu identifizieren (insb. falls sie Audio-Probleme haben)
- Schalten sie video aus, falls die Verbindung zu schlecht ist
- Wir legen einen Moodle-Kurs an, in dem sie sich austauschen koennen. Weitere Info via almaweb-email sobald der Kurs aktiv ist
Thema: Bi-Alignments
Selection pressures on the sequence and structure of an RNA or a protein my have independent causes. This may lead to a ``shift'' of an evolutionary conserved structure relative to the underlying sequence. As a consequence, homologous sequence position may appear in different structural contexts, while analogous structural features are formed by non-homologous sequence positions. Computationally, this situation is modeled as an alignment of two distinct alignments U and V of the same input pair. The alignment W of U and V then scores the shifts between the two alignments. Due to the circumstances, there will be no classroom teaching for this module. We will use an inverted classroom format instead:Below you find reading material for the project which you are requested to read and study by the dates listed below. Peter Stadler will be available for consultations via https://meet.jit.si/ at times listed below.
Themenübersicht
Aufgaben
- Implementation of the bi-alignment algorithm with linear gap costs (not optimized, for testing purposes)
- Implementation of the bi-alignment algorithm with affine gap costs (not optimized, for testing purposes)
- Implementation of the bi-alignment algorithm with affine gap costs using Carillo-Lipman style bounds.
- Benchmarking of the implementations.
- Application: search for evidence of shifts/incongruent evolution of protein secondary structures in the Pfam database.
Wichtig
Literatur