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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 ed...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688514/ https://www.ncbi.nlm.nih.gov/pubmed/19422723 http://dx.doi.org/10.1186/1471-2105-10-135 |
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author | Du, Pufeng Jia, Liyan Li, Yanda |
author_facet | Du, Pufeng Jia, Liyan Li, Yanda |
author_sort | Du, Pufeng |
collection | PubMed |
description | 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 . CONCLUSION: 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. |
format | Text |
id | pubmed-2688514 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26885142009-05-30 CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants Du, Pufeng Jia, Liyan Li, Yanda BMC Bioinformatics Software 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 . CONCLUSION: 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. BioMed Central 2009-05-08 /pmc/articles/PMC2688514/ /pubmed/19422723 http://dx.doi.org/10.1186/1471-2105-10-135 Text en Copyright © 2009 Du et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Du, Pufeng Jia, Liyan Li, Yanda CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants |
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 |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688514/ https://www.ncbi.nlm.nih.gov/pubmed/19422723 http://dx.doi.org/10.1186/1471-2105-10-135 |
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