Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites.
BACKGROUND
Data representation and encoding are essential for classification of protein sequences with artificial neural networks (ANN). Biophysical properties are appropriate for low dimensional encoding of protein sequence data. However, in general there is no a priori knowledge of the relevant properties for extraction of representative features.


RESULTS
An adaptive encoding artificial neural network (ACN) for recognition of sequence patterns is described. In this approach parameters for sequence encoding are optimized within the same process as the weight vectors by an evolutionary algorithm. The method is applied to the prediction of signal peptide cleavage sites in human secretory proteins and compared with an established predictor for signal peptides.


CONCLUSIONS
Knowledge of physico-chemical properties is not necessary for training an ACN. The advantage is a low dimensional data representation leading to computational efficiency, easy evaluation of the detected features, and high prediction accuracy.


BACKGROUND
A cleavage site prediction server is located at the Humboldt University http://itb.biologie.hu-berlin.de/ approximately jo/sig-cleave/ACNpredictor.cgi


BACKGROUND
jo@itb.hu-berlin.de; berndj@zedat.fu-berlin.de
Jagla
B
B
Freie Universität Berlin, Institut für Med./Techn. Physik und Lasermedizin, Krahmerstrasse 6-10, 12045 Berlin, Germany.
Schuchhardt
J
J
D001665:Binding Sites; D006801:Humans; D016571:Neural Networks, Computer; D021382:Protein Sorting Signals / Q000032:analysis*; D011506:Proteins / Q000032:analysis
D021382:Protein Sorting Signals; D011506:Proteins