Bioinformatisches Praktikum
Sequenzanalyse und Genomik & Fortgeschrittene Methoden in der Bioinformatik
Das Praktikum ist beendet. Die Protokolle bitte nach den Nacharbeiten an Alex schicken. Diese sind dann hier zu finden.
Start: 19.01.2009, 10 Uhr s.t.
Ort: Pool 320.6, Härtelstr. 16-18
Praktikumsvorbesprechung: done.
Praktikumsendbesprechung: done.
Protein Homology Detection
- SR Proteine splice regulators, origin: Eukaryota, search for secondary losses
- V(D)J Rekombination RAG1, RAG2, origin: jawed vertebrates, jaw vs. jawless
- miRNA Pathway Drosha, Dicer, Argonaute, Piwi, origin: Eukaryota, search for secondary losses
- RNA-bindende Proteine Mechanismus der Erkennung von RNA binding sites durch Proteine, Strukturinformation an der RNA binding sites
Literatur (z.T. auf Grund von Copyright-Bestimmungen nur innerhalb des Uni Netzes erreichbar! Bei Zugriffsproblemen bitte an einen der Betreuer wenden.)
- SR Proteine
- Co-evolution of the branch site and SR proteins in eukaryotes.
Plass M, Agirre E, Reyes D, Camara F, Eyras E.
Trends Genet. 2008 Dec;24(12):590-4. Epub 2008 Nov 5. - Plant SR proteins and their functions.
Barta A, Kalyna M, Lorkovic ZJ.
Curr Top Microbiol Immunol. 2008;326:83-102.
Review. - V(D)J Rekombination
- Antigen receptor genes and the evolution of a recombinase.
Schatz DG.
Semin Immunol. 2004 Aug;16(4):245-56.
Review. - microRNA Pathway
- Plant ARGONAUTES.
Vaucheret H.
Trends Plant Sci. 2008 Jul;13(7):350-8. Epub 2008 May 26.
Review. - The Argonaute protein family.
Höck J, Meister G.
Genome Biol. 2008;9(2):210. Epub 2008 Feb 26.
Review. - The evolution of core proteins involved in microRNA biogenesis.
Murphy D, Dancis B, Brown JR.
BMC Evol Biol. 2008 Mar 25;8:92. - Specialization and evolution of endogenous small RNA pathways.
Chapman EJ, Carrington JC.
Nat Rev Genet. 2007 Nov;8(11):884-96.
Review. - Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals.
Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP.
Nature. 2008 Oct 30;455(7217):1193-7. Epub 2008 Oct 1. - Origins and evolution of eukaryotic RNA interference.
Shabalina SA, Koonin EV.
Trends Ecol Evol. 2008 Oct;23(10):578-87. Epub 2008 Aug 18. - RNA-bindende Proteine
- Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.
Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO.
PLoS Biol. 2008 Oct 28;6(10):e255. - Drosophila development: homeodomains and translational control.
Zamore PD, Lehmann R.
Curr Biol. 1996 Jul 1;6(7):773-5.
Review. - allgemeine Literatur
- The limits of protein sequence comparison?
Pearson WR, Sierk ML.
Curr Opin Struct Biol. 2005 Jun;15(3):254-60.
Review. - The WWWH of remote homolog detection: the state of the art.
Fariselli P, Rossi I, Capriotti E, Casadio R.
Brief Bioinform. 2007 Mar;8(2):78-87. Epub 2006 Sep 26.
Review.
- BLAST package (tblastn, PSI-tblastn)
- hmmer package (hmmpfam)