Bioinformatik von RNA- und Proteinstrukturen (Modul 10-202-2208)
News
Praktikum
The folding of RNAs highly depends on the temperature in which the
respective organism lives. The temperature rescales the energy
parameters used in structure prediction algorithms that are based on
energy optimization. In RNAfold, there is the parameter
-T,--temp=DOUBLE that adjusts the energy parameter according to a
given temperature (default: 37°C).
The question is, what happens if we want to compare the secondary
structures of related RNA sequences of species that live in
environments that differ significantly in their temperature. The
predicted secondary structures may als substantially differ although the
genes are homologous at primary sequence level and the consensus
structure would be meaningless..
This lab course aims to introduce the temperature parameter for all
input sequences into the RNAalifold program and benchmark the effect.
Das Praktikum findet wie folgt statt:
| Raum: | 109, Härtelstr. 16-18 |
| Zeit: | ganztägig |
| Datum: | 15.06.15 - 26.06.15 |
| Kernzeit: | 10-15 Uhr |
| Endbesprechung: | 03.07.15, 11.00-15.00 Uhr im Raum 015.1 |
Vorlesung, Übung
|
| Tag | Zeit | VL / Ü | Raum | Material | Thema |
|---|---|---|---|---|---|
| 10.04.15 | 10.00 - 12.00 Uhr | VL 01 | 109 | Material 01 | Organisatorisches, Einführung - Struktur von Biomoleküen |
| 13.04.15 | 10.00 - 12.00 Uhr | VL 02 | 109 | Material 02 | Das RNA folding problem |
| 17.04.15 | 13.00 - 15.30 Uhr | Ü 01 | 006 | nussinov.pl | Strukturen zählen, Nussinov implementieren |
| 20.04.15 | 10.00 - 12.00 Uhr | VL 03 | 109 | ||
| 24.04.15 | 10.00 - 12.00 Uhr | VL 04 | 109 | ||
| 27.04.15 | 10.00 - 12.00 Uhr | Ü 02 | 006 | ||
| 04.05.15 | 10.00 - 12.00 Uhr | VL 05 | 109 | Material 05 | Proteinstrukturen |
| 08.05.15 | 10.00 - 12.00 Uhr | VL 06 | 109 | Material 06, Wuchty_99a.pdf | Suboptimale Strukturen |
| 11.05.15 | 10.00 - 12.30 Uhr | Ü 03 | 006 | ||
| 18.05.15 | 10.00 - 12.00 Uhr | VL 07 | 109 | ||
| 22.05.15 | 10.00 - 12.00 Uhr | VL 08 | 109 | ||
| 29.05.15 | 13.00 - 15.30 Uhr | Ü 04 | 006 | ||
| 01.06.15 | 10.00 - 12.00 Uhr | VL 09 | 109 | ||
| 05.06.15 | 10.00 - 12.00 Uhr | VL 10 | 109 | ||
| 08.06.15 | 10.00 - 12.00 Uhr | Ü 05 | 006 | ||
| 12.06.15 | 10.00 - 12.00 Uhr | VL 11 | 109 |
Literatur
M. Höchsmann, T. Töller, R. Giegerich and S. Kurz (2003). Local Similarity in RNA Secondary Structures. CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics. S. 159.G.Steger (2003). Bioinformatik - Methoden zur Vorhersage von RNA- und Proteinstrukturen. Birkhäuser. ISBN 3-7643-6951-5
R.Durbin, S.Eddy, A. Krogh & G.Mitchison (1998). Biological sequence analysis. Cambridge University Press. ISBN 0-521-62971-3
Nussinov, R., Piecznik, G., Griggs, J. R. & Kleitman, D. J. (1978). Algorithms for loop matching. SIAM J Appl Math, 35, 68-82.
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, and Peter Schuster. Fast Folding and Comparison of RNA Secondary Structures. Monatsh.Chem. 125: 167-188 (1994).