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 | |
| State | Published - 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