Mining Cytochrome b561 proteins from plant genomes

Stephen O. Opiyo, Etsuko N. Moriyama

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

Cytochrome b561 (Cyt-b561) proteins are important for plant growth, development, and prevention of damage to plants. Because of their high sequence divergence, thorough mining of Cyt-b561 proteins from plant genomes are not easy. Currently there is only one Cyt-b561 gene found in the maize and none in the soybean genome. However, 22 have been identified in the Arabidopsis thaliana genome. We tested alignment-free protein classifiers based on partial least squares (PLS) and support vector machines to identify Cyt-b561. These classifiers performed better than profile hidden Markov models and PSI-BLAST. Using these classifiers we identified new Cyt-b561-related proteins from four plant genomes.

Original languageEnglish (US)
Pages (from-to)209-221
Number of pages13
JournalInternational Journal of Bioinformatics Research and Applications
Volume6
Issue number2
DOIs
Publication statusPublished - Jan 1 2010

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Keywords

  • Cytochrome b561
  • PLS
  • PSI-BLAST
  • SVMs
  • partial least squares
  • profile hidden Markov model
  • support vector machines

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Clinical Biochemistry
  • Health Information Management

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