Mining Cytochrome b561 proteins from plant genomes

Stephen O. Opiyo; Etsuko N. Moriyama

doi:10.1504/IJBRA.2010.032122

Mining Cytochrome b561 proteins from plant genomes

Stephen O. Opiyo, Etsuko N. Moriyama

Biological Sciences

Research output: Contribution to journal › Article

4 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 language	English (US)
Pages (from-to)	209-221
Number of pages	13
Journal	International Journal of Bioinformatics Research and Applications
Volume	6
Issue number	2
DOIs	https://doi.org/10.1504/IJBRA.2010.032122
State	Published - Jan 1 2010

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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Opiyo, S. O., & Moriyama, E. N. (2010). Mining Cytochrome b561 proteins from plant genomes. International Journal of Bioinformatics Research and Applications, 6(2), 209-221. https://doi.org/10.1504/IJBRA.2010.032122

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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.",

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