Mining Cytochrome b561 proteins from plant genomes.
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.
Opiyo
Stephen O
SO
School of Biological Sciences, University of Nebraska-Lincoln, NE 68588, USA. sopiyo@unlserve.unl.edu
Moriyama
Etsuko N
EN
D003573:Cytochrome b Group / Q000737:chemistry / Q000235:genetics*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D018745:Genome, Plant; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*
D003573:Cytochrome b Group; D010940:Plant Proteins; C023646:cytochrome b561