Abstract

Many domains have a stake in the development of reliable systems for automatic protein classification. Of particular interest in recent studies of automatic protein classification is the exploration of new methods for extracting features from a protein that enhance classification for specific problems. These methods have proven very useful in one or two domains, but they have failed to generalize well across several domains (i.e. classification problems). In this paper, we evaluate several feature extraction approaches for representing proteins with the aim of sequence-based protein classification. Several protein representations are evaluated, those starting from: the position specific scoring matrix (PSSM) of the proteins; the amino-acid sequence; a matrix representation of the protein, of dimension (length of the protein) ×20, obtained using the substitution matrices for representing each amino-acid as a vector. A valuable result is that a texture descriptor can be extracted from the PSSM protein representation which improves the performance of standard descriptors based on the PSSM representation. Experimentally, we develop our systems by comparing several protein descriptors on nine different datasets. Each descriptor is used to train a support vector machine (SVM) or an ensemble of SVM. Although different stand-alone descriptors work well on some datasets (but not on others), we have discovered that fusion among classifiers trained using different descriptors obtains a good performance across all the tested datasets.

Department(s)

Information Technology and Cybersecurity

Document Type

Article

DOI

https://doi.org/10.1007/s00726-012-1416-6

Rights Information

© 2014 The authors. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Publication Date

2013

Journal Title

Amino Acids

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