Nucleic Acids Research, 2001, Vol. 29, No. 16 e82
© 2001 Oxford University Press
Chloroplast transit peptide prediction: a peek inside the black box
University of Pennsylvania Department of Computer and Information Science, 556 Moore Building, 200 S. 33rd Street, Philadelphia, PA 19104-6389, USA and 1Department of Biology, Goddard Laboratories, University of Pennsylvania, Philadelphia, PA 19104-6018, USA
Previous work in predicting protein localization to the chloroplast organelle in plants led to the development of an artificial neural network-based approach capable of remarkable accuracy in its prediction (ChloroP). A common criticism against such neural network models is that it is difficult to interpret the criteria that are used in making predictions. We address this concern with several new prediction methods that base predictions explicitly on the abundance of different amino acid types in the N-terminal region of the protein. Our successful prediction accuracy suggests that ChloroP uses little positional information in its decision-making; an unexpected result given the elaborate ChloroP input scheme. By removing positional information, our simpler methods allow us to identify those amino acids that are useful for successful prediction. The identification of important sequence features, such as amino acid content, is advantageous if one of the goals of localization predictors is to gain an understanding of the biological process of chloroplast localization. Our most accurate predictor combines principal component analysis and logistic regression. Web-based prediction using this method is available online at http://apicoplast.cis.upenn.edu/pclr/.
* To whom correspondence should be addressed. Tel: +1 215 735 9167; Fax: +1 215 898 0587; Email: ais{at}gradient.cis.upenn.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. Yoshihara, K. Inoue, D. Schichnes, S. Ruzin, W. Inwood, and S. Kustu An Rh1-GFP Fusion Protein Is in the Cytoplasmic Membrane of a White Mutant Strain of Chlamydomonas reinhardtii Mol Plant, November 14, 2008; (2008) ssn074v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Myouga, C. Hosoda, T. Umezawa, H. Iizumi, T. Kuromori, R. Motohashi, Y. Shono, N. Nagata, M. Ikeuchi, and K. Shinozaki A Heterocomplex of Iron Superoxide Dismutases Defends Chloroplast Nucleoids against Oxidative Stress and Is Essential for Chloroplast Development in Arabidopsis PLANT CELL, November 1, 2008; 20(11): 3148 - 3162. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Ono, A. Sakai, K. Takechi, S. Takio, M. Takusagawa, and H. Takano NtPolI-like1 and NtPolI-like2, Bacterial DNA Polymerase I Homologs Isolated from BY-2 Cultured Tobacco Cells, Encode DNA Polymerases Engaged in DNA Replication in Both Plastids and Mitochondria Plant Cell Physiol., December 1, 2007; 48(12): 1679 - 1692. [Abstract] [Full Text] [PDF]
|
|