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Using pseudo amino acid composition to predict protein subcellular location: approached with amino acid composition distribution

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Summary.

In the Post Genome Age, there is an urgent need to develop the reliable and effective computational methods to predict the subcellular localization for the explosion of newly found proteins. Here, a novel method of pseudo amino acid (PseAA) composition, the so-called “amino acid composition distribution” (AACD), is introduced. First, a protein sequence is divided equally into multiple segments. Then, amino acid composition of each segment is calculated in series. After that, each protein sequence can be represented by a feature vector. Finally, the feature vectors of all sequences thus obtained are further input into the multi-class support vector machines to predict the subcellular localization. The results show that AACD is quite effective in representing protein sequences for the purpose of predicting protein subcellular localization.

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Abbreviations

AAC:

amino acid composition

AACD:

amino acid composition distribution

5CV:

5-fold cross validation

DAG:

directed acyclic graph

DPC:

dipeptide composition

KNN:

k-nearest neighbor

OVO:

one-versus-one

OVR:

one-versus-rest

PPC:

polypeptide composition

PseAA:

pseudo amino acid composition

RBF:

radial basis function

SVM:

support vector machines

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Authors and Affiliations

  1. School of Computer Science and Engneering, Northwestern Polytechnical University, Xi’an, China

    J.-Y. Shi

  2. School of Automation, Northwestern Polytechnical University, Xi’an, China

    S.-W. Zhang & Q. Pan

  3. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA

    G.-P. Zhou

Authors
  1. J.-Y. Shi
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  2. S.-W. Zhang
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  3. Q. Pan
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  4. G.-P. Zhou
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Authors’ address: Shao-Wu Zhang, College of Automation control, Northwestern Polytechnical University, 127 YouYi West Rd., Xi’an 710072, Shaanxi, China

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Shi, JY., Zhang, SW., Pan, Q. et al. Using pseudo amino acid composition to predict protein subcellular location: approached with amino acid composition distribution. Amino Acids 35, 321–327 (2008). https://doi.org/10.1007/s00726-007-0623-z

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  • DOI: https://doi.org/10.1007/s00726-007-0623-z

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