Table 3 Databases for predicting RNA m6A modification.
From: The role of N6-methyladenosine-modified non-coding RNAs in the pathological process of human cancer
Databases | Introduction | Strength | Motif restriction | Reference (PMID) |
|---|---|---|---|---|
m6Acomet | The m6Acomet supports direct query for the predicted biological roles of m6A modifications and the m6A sites exhibiting co-methylated patterns at the epitranscriptome level. | The website has a high accuracy in predicting m6A; The prediction results in the co-methylation network suggested higher biological significance. | DRACH | 31046660 |
m6A2Target | m6A2Target is a comprehensive wibsite for targets of m6A-related enzymes. | The m6A2Target is the earliest detailed website for m6A writers, erasers and readers (WERs) target genes. | Â | 32392583 |
m6AVar | m6AVar is a website of functional variants involved in m6A modification | The m6AVar can serve as a useful resource for annotating variants and identifying disease-causing variants. | DRACH | 29036329 |
WHISTLE | WHISTLE is a high-accuracy tool for predicting m6A. | The WHISTLE integrated RNA methylation profiles, gene expression profiles and protein-protein interaction data to make the query convenient of high-accuracy information of the m6A modifications. | RRACH | 30993345 |
iRNA-Methyl | iRNA-Methyl identified m6A sites using pseudo nucleotide composition | iRNA-Methyl holds very high potential to become a useful tool for analyzing m6A in whole genome. | GAC | 26314792 |
pRNAm-PC | pRNAm-PC can predict m6A modifications | The overall accuracy and stability of the pRNAm-PC are superior to other existing prediction tools. And it can be used to investigate other functions of RNA. | GAC | 26748145 |
Targetm6A | Targetm6A can identify m6A modifications from RNA sequences through position-specific nucleotide propensities and a support vector machine | TargetM6A could rapidly and accurately target m6A modifications solely from the primary RNA sequences. | Â | 27552763 |
iRNA(m6A)-PseDNC | iRNA(m6A)-PseDNC can identify N6-methyladenosine sites via pseudo dinucleotide composition | Its performance is superior to existing methods. | Â | 30201554 |
m6APred-EL | m6APred-EL can identify m6A modification using ensemble learning | M6APred-EL can accurately predict the site information of m6A modification. | GAC | 30081234 |
AthMethPre | AthMethPre is a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana. | The server also provides a comprehensive database of predicted transcriptome-wide m6A sites and curated m6A-seq peaks from the literature for query and visualization. | Â | 27550167 |
RFAthm6A | RFAthM6A is a new tool for predicting m6A sites in Arabidopsis thaliana. | RFAthm6A can deeply analyze the relevant information of m6A modification. | Â | 29340952 |
m6AMRFS | m6AMRFS is a robust predicting tool for m6A modification based on sequence-based features | M6AMRFS is the first tool that can be used for the identification of m6A sites in multiple species. | Â | 30410501 |
CVm6A | CVm6A is a visualization and research tool for m6A modification in cell lines | The specificity of CVm6A could significantly contribute to the research for the function and regulation of cell-dependent m6A modification in disease and development. | RRACH | 30781586 |
RMBase v2.0 | RMBase v2.0 can depict RNA modification at the transcriptome level | It allows for the global research of among RNA modification and offers us abundant interfaces and graphic visualizations to facilitate analyses of the massive modification sites in normal tissues and cancer cells. | RACH | 29040692 |
SRAMP | SRAMP: prediction of mammalian m6A sites based on sequence-derived features. | It could recognize the specific sequence features of the m6A-enriched regions and provide reasonable prediction results. | DRACH | 26896799 |
DEEPM6ASeq | DeepM6ASeq can predict and characterize the m6A-containing sequences through deep learning. | DeepM6ASeq could predict and characterize m6A-containing sequences based on miCLIP-Seq data at single-base resolution level. | Â | 30598068 |
m6A-Atlas | The m6A-Atlas is a comprehensive tool for investigating the m6A modification. | The m6A-Atlas is a high reliable tool for unrevealing m6A modification and the quantitative condition-specific epitranscriptome profiles estimated from abundant high-throughput sequencing samples in different tissues and cell lines. | DRACH | 32821938 |
