目前,已经有多个工具相继被开发出来预测RNA中的m6A甲基化位点,这些工具按文章发表时间顺序主要有(更多精彩请关注微信公众号:AIPuFuBio):
1. iRNA-Methyl
发表文章:Chen et al. iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseudo nucleotide composition. Analytical Biochemistry,2015
2. SRAMP
发表文章:Zhou et al. SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. Nucleic Acids Research, 2016
3. iRNAm5C-PseDNC
发表文章:Qiu et al. iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition. Oncotarget, 2017
4. M6AMRFS
发表文章:Qiang et al. M6AMRFS: Robust Prediction of N6-Methyladenosine Sites With Sequence-Based Features in Multiple Species. Frontiers in Genetics, 2018
5. M6APred-EL
发表文章:Wei et al. M6APred-EL: A Sequence-Based Predictor for Identifying N6-methyladenosine Sites Using Ensemble Learning. Molecular Therapy: Nucleic Acids, 2018
6. DeepM6ASeq
发表文章:Zhang et al. DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning. BMC Genomics, 2018
上面的这些软件可以预测RNA中的m6A甲基化位点,那么如何进一步注释m6A甲基化的功能呢?具体可用如下工具:
软件名称:m6Acomet
发表文章:Wu et al. m6Acomet: large-scale functional prediction of individual m6 A RNA methylation sites from an RNA comethylation network. BMC Bioinformatics, 2019
所以,大家如果对某条或某些RNA感兴趣,只需找到对应的RNA碱基序列,就可以利用本文中的提到的6款软件来预测RNA序列中潜在的m6A甲基化位点。如果需要进一步预测m6A甲基化位点的功能,则可利用如m6Acomet软件。这些软件可允许用户大规模预测RNA中m6A甲基化位点,克服了实验只能同时验证少量RNA序列的缺点。而且,这些软件预测的结果,可以进一步缩小实验验证的范围,从而节省研究时间和降低实验失败的风险。(更多精彩,可见大型免费综合生物信息学资源和工具平台AIPuFu:www.aipufu.com,关注微信公众号:AIPuFuBio)。
希望今天的内容对大家有用,会持续更新经典内容,欢迎留言~~
参考文献
1. Fu et al. Gene expression regulation mediated through reversible m⁶A RNA methylation, Nature Reviews Genetics, 2014
2. Roundtree et al. Dynamic RNA Modifications in Gene Expression Regulation, Cell, 2017
3. Lee et al. Emerging Roles of RNA Modification: m6 A and U-Tail, Cell, 2017
联系客服