Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn

Seminar

Speaker: Guangyou Duan, AG Bioinformatics

Title: Improved splice site prediction using sequence information and singular value decomposition

Time: Fri, Oct 29, 2010, 1pm

Place: MPI für Molekulare Pflanzenphysiologie, Room 0.21 in The Box

Abstract:
Splice site prediction is an important part of gene identification in eukaryotic genome. There have been many computational methods proposed for detecting splice site, whereas, computation time has received little attention. However, it is well known that how to fast annotate the genome is a key process in post-genomic era. In this study, we propose an improved method for splice site prediction. It employs WebLogo and first order Markov model to exploit the sequence conservation information, and then uses singular value decomposition (SVD) to reduce the dimension of the input feature for the classifier support vector machine (SVM). This novel approach has shown to be more efficient in generating results when compared with the best known method, IC Shapiro SVM. Our data show that it is ten times faster for acceptor site prediction and twenty times faster for donor splice site prediction.

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Past NLD Seminars (1994-2007) & (2008 ...)

Students' seminar: Theoretical Physics, PIK, Modeling & TSA Berlin-Potsdam-Colloquia: PhysGesellschaft Berlin, TU Berlin, Pro Physik, AIP, AEI, MPI-KGF, GFZ, HMI, PIK, AWI, Max Planck Institute for the History of Science, Mathematik, DPG Disputationen, & Vorschau UP

Udo Schwarz, Zentrum für Dynamik komplexer Systeme,
Universität Potsdam, Campus Golm Karl-Liebknecht-Str. 24, 14476 Potsdam, building 28, room 2.107
Phone: (+49-331) 977-1658, Fax : (+49-331) 977-1045

Email: Udo.Schwarz AT uni-potsdam.de

DFG SFB 1294

DFG Sonderforschungsbereich 1294 Data assimilation

DFG SPP 1488

DFG Schwerpunktprogramm 1488 Planetmag


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