Simple alignment-free methods for protein classification: A case study from G-protein-coupled receptors

Pooja K. Strope, Etsuko N. Moriyama

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Computational methods of predicting protein functions rely on detecting similarities among proteins. However, sufficient sequence information is not always available for some protein families. For example, proteins of interest may be new members of a divergent protein family. The performance of protein classification methods could vary in such challenging situations. Using the G-protein-coupled receptor superfamily as an example, we investigated the performance of several protein classifiers. Alignment-free classifiers based on support vector machines using simple amino acid compositions were effective in remote-similarity detection even from short fragmented sequences. Although it is computationally expensive, a support vector machine classifier using local pairwise alignment scores showed very good balanced performance. More commonly used profile hidden Markov models were generally highly specific and well suited to classifying well-established protein family members. It is suggested that different types of protein classifiers should be applied to gain the optimal mining power.

Original languageEnglish (US)
Pages (from-to)602-612
Number of pages11
Issue number5
StatePublished - May 2007
Externally publishedYes


  • Amino acid composition
  • G-protein-coupled receptors
  • Profile hidden Markov models
  • Protein classification
  • Support vector machines

ASJC Scopus subject areas

  • Genetics


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