Amino Acids

, Volume 30, Issue 1, pp 49–54

Using cellular automata images and pseudo amino acid composition to predict protein subcellular location

  • X. Xiao
  • S. Shao
  • Y. Ding
  • Z. Huang
  • K.-C. Chou
Article

DOI: 10.1007/s00726-005-0225-6

Cite this article as:
Xiao, X., Shao, S., Ding, Y. et al. Amino Acids (2006) 30: 49. doi:10.1007/s00726-005-0225-6

Summary.

The avalanche of newly found protein sequences in the post-genomic era has motivated and challenged us to develop an automated method that can rapidly and accurately predict the localization of an uncharacterized protein in cells because the knowledge thus obtained can greatly speed up the process in finding its biological functions. However, it is very difficult to establish such a desired predictor by acquiring the key statistical information buried in a pile of extremely complicated and highly variable sequences. In this paper, based on the concept of the pseudo amino acid composition (Chou, K. C. PROTEINS: Structure, Function, and Genetics, 2001, 43: 246–255), the approach of cellular automata image is introduced to cope with this problem. Many important features, which are originally hidden in the long amino acid sequences, can be clearly displayed through their cellular automata images. One of the remarkable merits by doing so is that many image recognition tools can be straightforwardly applied to the target aimed here. High success rates were observed through the self-consistency, jackknife, and independent dataset tests, respectively.

Keywords: Cellular automata images – Pseudo amino-acid composition – Protein subcellular location – Complexity – Covariant-discriminant algorithm 

Copyright information

© Springer-Verlag/Wien 2005

Authors and Affiliations

  • X. Xiao
    • 1
    • 2
  • S. Shao
    • 1
  • Y. Ding
    • 1
  • Z. Huang
    • 1
  • K.-C. Chou
    • 1
    • 3
  1. 1.Bioinformatics Research Center, Donghua UniversityShanghaiChina
  2. 2.Computer DepartmentJing-De-Zhen Ceramic InstituteJing-De-ZhenChina
  3. 3.Gordon Life Science InstituteSan DiegoU.S.A.

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