DOI: 10.31038/JMG.2020322

Short Commentary

In 2015 a very powerful web-server predictor has been established for identifying N⁶-methyladenosine (m⁶A), which is one of the most abundant modifications in RNA [1].

To see how the web-server is working, please do the following.

Step 1: Open the web server at http://lin.uestc.edu.cn/server/iRNA-Methyl and you will see the top page of the iRNA-Methyl predictor on your computer screen, as shown in Fig.1. Click on the Read Me button to see a brief introduction about the predictor and the caveat when using it.

Figure 1. A semi screenshot for the top page of iRNA-Methyl (Adapted from [1] with permission).

Step 2: Either type or copy/paste the query RNA sequences into the input box at the center of Fig.1. The input sequence should be in FASTA format.  For the examples of RNA sequences in FASTA format, click the Example button right above the input box.

Step 3: Click on the Submit button to see the predicted result. For example, if you use the query RNA sequences in the Example window as the input, you will see the following shown on the screen of your computer. (1) RNA sequence-1 contains 5 “GAC” (with adenine at its middle) consensus motifs, of which only those at the sequence positions 128 is predicted to be the methylation sites or  site, and all the others are not. (2) RNA sequence-2 contains 8 “GAC” consensus motifs, of which only those at the sequence positions 332 is predicted to be the methylation sites, while all the others are not. All these results are fully consistent with the experimental observations.

Step 4: Click on the Data button to download the datasets used to train and test the model.

Step 5: Click on the Citation button to find the relevant paper that document the detailed development and algorithm of iRNA-Methyl.

It is instructive to point out that the web-server predictor has been developed by strictly observing the guidelines of “Chou’s 5-steps rule” and hence have the following notable merits (see, e.g., [2–14] and three comprehensive review papers [15–17]: (1) crystal clear in logic development, (2) completely transparent in operation, (3) easily to repeat the reported results by other investigators, (4) with high potential in stimulating other sequence-analyzing methods, and (5) very convenient to be used by the majority of experimental scientists.

Moreover, it has not escaped our notice that during the development of iRNA-Methyl web-server, the approach of general pseudo amino acid components [18] or PseAAC [19] had been utilized and hence its accuracy would be much higher than its counterparts, as concurred by many investigators [15, 18–266].

It is anticipated that iRNA-Methyl may become a useful high throughput tool for conducting genome analysis as well as drug development.

For the remarkable and awesome roles of the “5-steps rule” in driving proteome, genome analyses and drug development, see a series of recent papers [16, 17, 267–276] where the rule and its wide applications have been very impressively presented from various aspects or at different angles.

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