m6ASNP: a tool for annotating genetic variants by m(6)A function

BACKGROUND: Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m(6)A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m(6)A modifications are involved in many diseases. FINDINGS: In this study, we present a user-friendly web server called “m6ASNP” that is dedicated to the identification of genetic variants that target m(6)A modification sites. A random forest model was implemented in m6ASNP to predict whether the methylation status of an m(6)A site is altered by the variants that surround the site. In m6ASNP, genetic variants in a standard variant call format (VCF) are accepted as the input data, and the output includes an interactive table that contains the genetic variants annotated by m(6)A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and to annotate the genetic variants. CONCLUSIONS: We believe that m6ASNP is a very convenient tool that can be used to boost further functional studies investigating genetic variants. The web server “m6ASNP” is implemented in JAVA and PHP and is freely available at [60].