Conditional random fields for the prediction of signal peptide cleavage sites

Man Wai Mak, Sun Yuan Kung

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations

Abstract

Correct prediction of signal peptide cleavage sites has a significant impact on drug design. State-of-the-art approaches to cleavage site prediction typically use generative models (such as HMMs) to represent the statistics of amino acid sequences or use neural networks to detect the changes in short amino-acid segments along a query sequence. By formulating cleavage site prediction as a sequence labeling problem, this paper demonstrates how conditional random fields (CRFs) can be applied to cleavage site prediction. The paper also demonstrates how amino acid properties can be exploited and incorporated into the CRFs to boost prediction performance. Results show that the performance of CRFs is comparable to that of a state-of-the-art predictor (SignalP V3.0). Further performance improvement was observed when the decisions of SignalP and the CRF-based predictor are fused.

Original languageEnglish (US)
Title of host publication2009 IEEE International Conference on Acoustics, Speech, and Signal Processing - Proceedings, ICASSP 2009
Pages1605-1608
Number of pages4
DOIs
StatePublished - Sep 23 2009
Event2009 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2009 - Taipei, Taiwan, Province of China
Duration: Apr 19 2009Apr 24 2009

Publication series

NameICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
ISSN (Print)1520-6149

Other

Other2009 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2009
CountryTaiwan, Province of China
CityTaipei
Period4/19/094/24/09

All Science Journal Classification (ASJC) codes

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

Keywords

  • Cleavage sites
  • Conditional random fields
  • Discriminative models
  • Protein sequences
  • Signal peptides

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  • Cite this

    Mak, M. W., & Kung, S. Y. (2009). Conditional random fields for the prediction of signal peptide cleavage sites. In 2009 IEEE International Conference on Acoustics, Speech, and Signal Processing - Proceedings, ICASSP 2009 (pp. 1605-1608). [4959906] (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings). https://doi.org/10.1109/ICASSP.2009.4959906