[A novel method of the genome-wide prediction for the target genes and its application].
Based on the protein databases of several model species, this study developed a new method of the Genome-wide prediction for the target genes, using Hidden Markov model by Perl programming. The advantages of this method are high throughput, high quality and easy prediction, especially in the case of multi-domains proteins families. By this method, we predicted the PPR and TPR proteins families in whole genome of several model species. There were 536 PPR proteins and 199 TPR proteins in Oryza sativa ssp. japonica, 519 PPR proteins and 177 TPR proteins in Oryza sativa L. ssp. indica, 735 PPR proteins and 292 TPR proteins in Arabidopsis thaliana, 6 PPR proteins and 32 TPR proteins in Cyanidioschyzon merolae. Synechococcus and Thermophilic archaebacterium did not have PPR proteins. By contrast, 10 TPR proteins were found in Synechococcus and 4 TPR proteins were found in Thermophilic archaebacterium. Moreover, of these results, some further bioinformatics analyses were conducted.
Zhang
Jing-Jing
JJ
Key Laboratory of Ministry of Education for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China. zjj33@yahoo.com.cn
Feng
Jing
J
Zhu
Ying-Guo
YG
Li
Yang-Sheng
YS
D001426:Bacterial Proteins / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D016678:Genome / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics
D001426:Bacterial Proteins; D010940:Plant Proteins