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RAMPred: identifying the N1-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... Full description

Journal Title: Scientific Reports 2016, Vol.6
Main Author: Wei Chen
Other Authors: Pengmian Feng , Hua Tang , Hui Ding , Hao Lin
Format: Electronic Article Electronic Article
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ID: ISSN: ; E-ISSN: 2045-2322 ; DOI: 10.1038/srep31080
Link: http://dx.doi.org/10.1038/srep31080
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recordid: nature_a10.1038/srep31080
title: RAMPred: identifying the N1-methyladenosine sites in eukaryotic transcriptomes
format: Article
creator:
  • Wei Chen
  • Pengmian Feng
  • Hua Tang
  • Hui Ding
  • Hao Lin
subjects:
  • Article
ispartof: Scientific Reports, 2016, Vol.6
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 .
language:
source:
identifier: ISSN: ; E-ISSN: 2045-2322 ; DOI: 10.1038/srep31080
fulltext: fulltext
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  • 2045-2322
  • 20452322
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descriptionN 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 .
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