Fortgeschrittene Methoden in der Bioinformatik (10-INF-BIO4)

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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
Neu/Aktuell: Nach der Besprechung:
  • 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

VLDatumRaumUhrzeitThemaLiteratur
01 *** *** *** Introduction to Incongruent Evolution Waldl et al. BioArXiv preprint 2019
Waldl et al, Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
02 *** *** *** Some theoretical background on multiple (sequence) alignments
and alignments of alignments 		Berkemer et al, Compositional Structure of Alignments
John Kececioglu, Notes on a multiple alignment cost-bound of Carrillo and Lipman
03 *** *** *** Alignment of Alignments with Affine Gap Costs John Kececioglu, Dean Starrett Aligning alignments exactly RECOMB 2004 Preprint version
04 *** *** *** Bi-Alignments mit Affinen Gap Kosten Stadler & Will. Bi-Alignments with Affine Gaps Costs
05 *** *** *** Bi-Alignment für RNA Strukturen Waldl et al Incongruences Between Sequence and Secondary Structure Alignments of Nucleic Acids (preliminary version)
06 *** *** *** Application to Protein Secondary Structures Yamg et al: Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
Resource: Protein Secondary Structure Prediction Software
Resource: an overview from Uni Hamburg
*** *** *** Praktischen Aufgabenstellung/Projektbeschreibung Work Program
Plenar-Besprechung 1Mitte/Ende Mai R 109 xx:00-xx:00
Plenar-Besprechung 2Ende Juni R 109 xx:00-xx:00

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

Daten