CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants
<p>Abstract</p> <p>Background</p> <p>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 chloropla...
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| Format: | Article |
| Language: | English |
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BMC
2009-05-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/10/135 |
| _version_ | 1818759037513105408 |
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| author | Li Yanda Jia Liyan Du Pufeng |
| author_facet | Li Yanda Jia Liyan Du Pufeng |
| author_sort | Li Yanda |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>in vivo </it>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.</p> <p>Results</p> <p>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 <url>http://bioinfo.au.tsinghua.edu.cn/pure</url>.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-18T06:36:21Z |
| format | Article |
| id | doaj.art-7019098c47ee49bb8bfea8023b9dbe77 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T06:36:21Z |
| publishDate | 2009-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-7019098c47ee49bb8bfea8023b9dbe772022-12-21T21:17:46ZengBMCBMC Bioinformatics1471-21052009-05-0110113510.1186/1471-2105-10-135CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plantsLi YandaJia LiyanDu Pufeng<p>Abstract</p> <p>Background</p> <p>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 <it>in vivo </it>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.</p> <p>Results</p> <p>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 <url>http://bioinfo.au.tsinghua.edu.cn/pure</url>.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/10/135 |
| spellingShingle | Li Yanda Jia Liyan Du Pufeng CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants BMC Bioinformatics |
| title | CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants |
| title_full | CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants |
| title_fullStr | CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants |
| title_full_unstemmed | CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants |
| title_short | CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants |
| title_sort | cure chloroplast a chloroplast c to u rna editing predictor for seed plants |
| url | http://www.biomedcentral.com/1471-2105/10/135 |
| work_keys_str_mv | AT liyanda curechloroplastachloroplastctournaeditingpredictorforseedplants AT jialiyan curechloroplastachloroplastctournaeditingpredictorforseedplants AT dupufeng curechloroplastachloroplastctournaeditingpredictorforseedplants |