CURE-Chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants.
BACKGROUND
RNA editing is a type of post-transcriptional modification of RNA and belongs to the class of mechanisms that contribute to the complexity of transcriptomes. C-to-U RNA editing is commonly observed in plant mitochondria and chloroplasts. The in vivo mechanism of recognizing C-to-U RNA editing sites is still unknown. In recent years, many efforts have been made to computationally predict C-to-U RNA editing sites in the mitochondria of seed plants, but there is still no algorithm available for C-to-U RNA editing site prediction in the chloroplasts of seed plants.


RESULTS
In this paper, we extend our algorithm CURE, which can accurately predict the C-to-U RNA editing sites in mitochondria, to predict C-to-U RNA editing sites in the chloroplasts of seed plants. The algorithm achieves over 80% sensitivity and over 99% specificity. We implement the algorithm as an online service called CURE-Chloroplast http://bioinfo.au.tsinghua.edu.cn/pure.


CONCLUSIONS
CURE-Chloroplast is an online service for predicting the C-to-U RNA editing sites in the chloroplasts of seed plants. The online service allows the processing of entire chloroplast genome sequences. Since CURE-Chloroplast performs very well, it could be a helpful tool in the study of C-to-U RNA editing in the chloroplasts of seed plants.
MOE Key Laboratory of Bioinformatics and Bioinformatics Div. TNLIST/Department of Automation, Tsinghua University, Beijing 100084, PR China. dpf05@mails.tsinghua.edu.cn
Pufeng
P
Du
Liyan
L
Jia
Yanda
Y
Li
D000465:Algorithms; D030541:Databases, Genetic; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000235:genetics; D017393:RNA Editing / Q000235:genetics*; D018747:RNA, Chloroplast / Q000737:chemistry* / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D012639:Seeds / Q000378:metabolism
D018747:RNA, Chloroplast; D018749:RNA, Plant