Mining Cytochrome b561 proteins from plant genomes
by Stephen O. Opiyo, Etsuko N. Moriyama
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 6, No. 2, 2010

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.

Online publication date: Wed, 10-Mar-2010

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