open access

https://hdl.handle.net/2115/39796

Fusion of Conditional Random Field and SignalP for Protein Cleavage Site Prediction

英語

protein sequences

2009-10-04

Asia-Pacific Signal and Information Processing Association, 2009 Annual Summit and Conference, International Organizing Committee

Proceedings : APSIPA ASC 2009 : Asia-Pacific Signal and Information Processing Association, 2009 Annual Summit and Conference

716-721

APSIPA ASC 2009: Asia-Pacific Signal and Information Processing Association, 2009 Annual Summit and Conference. 4-7 October 2009. Sapporo, Japan. Oral session: Intelligent Circuits and Systems (7 October 2009).

Prediction of protein cleavage sites is an important step in drug design. Recent research has demonstrated that conditional random fields are capable of predicting the cleavage site locations of signal peptides, and their performance is comparable to that of SignalP - a state-of-the-art predictor based on hidden Markov models and neural networks. This paper investigates the degree of complementarity between CRF-based predictors and SignalP and proposes using the complementary properties to fuse the two predictors. It was found that about 40% of the sequences that are incorrectly predicted by SignalP can be correctly predicted by CRF, and that about 30% of the sequences that are incorrectly predicted by CRF can be correctly predicted by SignalP. This suggests that the two predictors complement each other. The paper also shows that the performance of CRF can be further improved by constructing the state features from spatially dispersed amino acids in the training sequences.

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