iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites
RNA modifications are additions of chemical groups to nucleotides or their local structural changes. Knowledge about the occurrence sites of these modifications is essential for in-depth understanding of the biological functions and mechanisms and for treating some genomic diseases as well. With the...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2018-06-01
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| Series: | Molecular Therapy: Nucleic Acids |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S216225311830043X |
| _version_ | 1817992261056593920 |
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| author | Wei Chen Pengmian Feng Hui Yang Hui Ding Hao Lin Kuo-Chen Chou |
| author_facet | Wei Chen Pengmian Feng Hui Yang Hui Ding Hao Lin Kuo-Chen Chou |
| author_sort | Wei Chen |
| collection | DOAJ |
| description | RNA modifications are additions of chemical groups to nucleotides or their local structural changes. Knowledge about the occurrence sites of these modifications is essential for in-depth understanding of the biological functions and mechanisms and for treating some genomic diseases as well. With the avalanche of RNA sequences generated in the post-genomic age, many computational methods have been proposed for identifying various types of RNA modifications one by one. However, so far no method whatsoever has been developed for simultaneously identifying several different types of RNA modifications. To address such a challenge, we developed a predictor called “iRNA-3typeA,” by which we can simultaneously identify the occurrence sites of the following three most frequently observed modifications in RNA: (1) N1-methyladenosine (m1A), (2) N6-methyladenosine (m6A), and (3) adenosine to inosine (A-to-I). It has been shown via rigorous cross-validations for the RNA sequences from Homo sapiens and Mus musculus transcriptomes that the success rates achieved by the powerful new predictor are quite high. For the convenience of broad experimental scientists, a user-friendly web server for iRNA-3typeA has been established at http://lin-group.cn/server/iRNA-3typeA/. It is anticipated that iRNA-3typeA may become a useful high throughput tool for genome analysis. |
| first_indexed | 2024-04-14T01:23:08Z |
| format | Article |
| id | doaj.art-fcc395051eb74770802b9043cd224105 |
| institution | Directory Open Access Journal |
| issn | 2162-2531 |
| language | English |
| last_indexed | 2024-04-14T01:23:08Z |
| publishDate | 2018-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj.art-fcc395051eb74770802b9043cd2241052022-12-22T02:20:33ZengElsevierMolecular Therapy: Nucleic Acids2162-25312018-06-0111C46847410.1016/j.omtn.2018.03.012iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine SitesWei Chen0Pengmian Feng1Hui Yang2Hui Ding3Hao Lin4Kuo-Chen Chou5Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, ChinaHebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063000, ChinaKey Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, ChinaKey Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, ChinaKey Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, ChinaKey Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, ChinaRNA modifications are additions of chemical groups to nucleotides or their local structural changes. Knowledge about the occurrence sites of these modifications is essential for in-depth understanding of the biological functions and mechanisms and for treating some genomic diseases as well. With the avalanche of RNA sequences generated in the post-genomic age, many computational methods have been proposed for identifying various types of RNA modifications one by one. However, so far no method whatsoever has been developed for simultaneously identifying several different types of RNA modifications. To address such a challenge, we developed a predictor called “iRNA-3typeA,” by which we can simultaneously identify the occurrence sites of the following three most frequently observed modifications in RNA: (1) N1-methyladenosine (m1A), (2) N6-methyladenosine (m6A), and (3) adenosine to inosine (A-to-I). It has been shown via rigorous cross-validations for the RNA sequences from Homo sapiens and Mus musculus transcriptomes that the success rates achieved by the powerful new predictor are quite high. For the convenience of broad experimental scientists, a user-friendly web server for iRNA-3typeA has been established at http://lin-group.cn/server/iRNA-3typeA/. It is anticipated that iRNA-3typeA may become a useful high throughput tool for genome analysis.http://www.sciencedirect.com/science/article/pii/S216225311830043XRNA modificationN1-methyladenosineN6-methyladenosineadenosine to inosine editingfive-step rulesweb server |
| spellingShingle | Wei Chen Pengmian Feng Hui Yang Hui Ding Hao Lin Kuo-Chen Chou iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites Molecular Therapy: Nucleic Acids RNA modification N1-methyladenosine N6-methyladenosine adenosine to inosine editing five-step rules web server |
| title | iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites |
| title_full | iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites |
| title_fullStr | iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites |
| title_full_unstemmed | iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites |
| title_short | iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites |
| title_sort | irna 3typea identifying three types of modification at rna s adenosine sites |
| topic | RNA modification N1-methyladenosine N6-methyladenosine adenosine to inosine editing five-step rules web server |
| url | http://www.sciencedirect.com/science/article/pii/S216225311830043X |
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