iDNA6mA-PseKNC: Identifying DNA N⁶-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC

Highlights

• A bioinformatics tool called iDNA6mA-PseKNC was developed for identifying N⁶-methyladenine (6mA) sites in DNA sequences.

• This is the first computational tool ever established for this purpose

• Rigorous cross-validations have indicated that the predictor's sensitivity, specificity, accuracy, and stability are all quite high.

• A user-friendly web-server for the predictor has been established by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

Abstract

N⁶-methyladenine (6mA) is one kind of post-replication modification (PTM or PTRM) occurring in a wide range of DNA sequences. Accurate identification of its sites will be very helpful for revealing the biological functions of 6mA, but it is time-consuming and expensive to determine them by experiments alone. Unfortunately, so far, no bioinformatics tool is available to do so. To fill in such an empty area, we have proposed a novel predictor called iDNA6mA-PseKNC that is established by incorporating nucleotide physicochemical properties into Pseudo K-tuple Nucleotide Composition (PseKNC). It has been observed via rigorous cross-validations that the predictor's sensitivity (Sn), specificity (Sp), accuracy (Acc), and stability (MCC) are 93%, 100%, 96%, and 0.93, respectively. For the convenience of most experimental scientists, a user-friendly web server for iDNA6mA-PseKNC has been established at http://lin-group.cn/server/iDNA6mA-PseKNC, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.