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RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes
N(1)-methyladenosine (m(1)A) is a prominent RNA modification involved in many biological processes. Accurate identification of m(1)A site is invaluable for better understanding the biological functions of m(1)A. However, limitations in experimental methods preclude the progress towards the identific...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980636/ https://www.ncbi.nlm.nih.gov/pubmed/27511610 http://dx.doi.org/10.1038/srep31080 |
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author | Chen, Wei Feng, Pengmian Tang, Hua Ding, Hui Lin, Hao |
author_facet | Chen, Wei Feng, Pengmian Tang, Hua Ding, Hui Lin, Hao |
author_sort | Chen, Wei |
collection | PubMed |
description | N(1)-methyladenosine (m(1)A) is a prominent RNA modification involved in many biological processes. Accurate identification of m(1)A site is invaluable for better understanding the biological functions of m(1)A. However, limitations in experimental methods preclude the progress towards the identification of m(1)A site. As an excellent complement of experimental methods, a support vector machine based-method called RAMPred is proposed to identify m(1)A sites in H. sapiens, M. musculus and S. cerevisiae genomes for the first time. In this method, RNA sequences are encoded by using nucleotide chemical property and nucleotide compositions. RAMPred achieves promising performances in jackknife tests, cross cell line tests and cross species tests, indicating that RAMPred holds very high potential to become a useful tool for identifying m(1)A sites. For the convenience of experimental scientists, a web-server based on the proposed model was constructed and could be freely accessible at http://lin.uestc.edu.cn/server/RAMPred. |
format | Online Article Text |
id | pubmed-4980636 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-49806362016-08-19 RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes Chen, Wei Feng, Pengmian Tang, Hua Ding, Hui Lin, Hao Sci Rep Article N(1)-methyladenosine (m(1)A) is a prominent RNA modification involved in many biological processes. Accurate identification of m(1)A site is invaluable for better understanding the biological functions of m(1)A. However, limitations in experimental methods preclude the progress towards the identification of m(1)A site. As an excellent complement of experimental methods, a support vector machine based-method called RAMPred is proposed to identify m(1)A sites in H. sapiens, M. musculus and S. cerevisiae genomes for the first time. In this method, RNA sequences are encoded by using nucleotide chemical property and nucleotide compositions. RAMPred achieves promising performances in jackknife tests, cross cell line tests and cross species tests, indicating that RAMPred holds very high potential to become a useful tool for identifying m(1)A sites. For the convenience of experimental scientists, a web-server based on the proposed model was constructed and could be freely accessible at http://lin.uestc.edu.cn/server/RAMPred. Nature Publishing Group 2016-08-11 /pmc/articles/PMC4980636/ /pubmed/27511610 http://dx.doi.org/10.1038/srep31080 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Chen, Wei Feng, Pengmian Tang, Hua Ding, Hui Lin, Hao RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes |
title | RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes |
title_full | RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes |
title_fullStr | RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes |
title_full_unstemmed | RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes |
title_short | RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes |
title_sort | rampred: identifying the n(1)-methyladenosine sites in eukaryotic transcriptomes |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980636/ https://www.ncbi.nlm.nih.gov/pubmed/27511610 http://dx.doi.org/10.1038/srep31080 |
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