Fusion of cleavage site detection and pairwise alignment for fast subcellular localization

Man Wai Mak, Sun-Yuan Kung

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

Abstract

In recent years, homology-based and signal-based methods have been proposed for predicting the subcellular localization of proteins. While it has been known that homology-based methods can detect more subcellular locations than signal-based methods, the former generally requires a lot more computational resources during both training and prediction. The problem will become intractable for annotating large databases. One possible solution is to reduce the sequence length. This paper proposes to use the cleavage sites detected by signal-based methods (e.g., TargetP) to extract the sequence or profile segments that contain the most localization information for alignment. It was found that the method can reduce computation time of full-length alignment by 27-fold at a cost of only 8% reduction in prediction accuracy. Moreover, the method can increase the accuracy by 0.8% and at the same time reduce the computation time by 41%. Results also show that cutting the sequences at the cleavage sites detected by TargetP is better than cutting them at a fixed position.

Original languageEnglish (US)
Title of host publication2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
Pages573-576
Number of pages4
DOIs
StatePublished - Sep 16 2008
Event2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP - Las Vegas, NV, United States
Duration: Mar 31 2008Apr 4 2008

Publication series

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

Other

Other2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
CountryUnited States
CityLas Vegas, NV
Period3/31/084/4/08

All Science Journal Classification (ASJC) codes

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

Keywords

  • Cleavage sites
  • Pairwise alignment
  • Profile
  • Protein sequences
  • Subcellular localization
  • TargetP

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  • Cite this

    Mak, M. W., & Kung, S-Y. (2008). Fusion of cleavage site detection and pairwise alignment for fast subcellular localization. In 2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP (pp. 573-576). [4517674] (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings). https://doi.org/10.1109/ICASSP.2008.4517674