How to use the sRNATarget web server
To predict sRNA targets, a web interface containing three parts was provided for the users (Figure 1).
In first part (Step 1), some genome should be selected from the list box. Then, the NCBI code will be filled in the box automatically. Correspondently, all names of known sRNAs annotated by NCBI will be listed in the sRNA list box. For example, the code NC_000913 is provided if the genome Escherichia K12 substr MG1655 is chosen.
In second part (Step2), users can choose one or all sRNAs for target prediction. The selected sequences will be displayed in sRNA sequence box in FastA format. If users want to predict targets for new sRNA sequences, all new sRNA sequences should be pasted into the sRNA sequence box in FastA format.
In the third part (Step3), users should set up the threshold for the prediction results and give an email for the returned results. Because the prediction model consisted of 1000 classifiers, all 1000 classifiers were used to predict whether a sRNA-mRNA interaction exists or not. If there are 700 classifiers to predict the interaction as the positive sample, the score will be 0.7 (700/1000) etc. The default value is 0.5 (500/1000).
Finally, click the "Submit>>>" button, the webserver will do calculation automatically and return the results through the email. The prediction results can be accessed through the notification email (Figure 2). There are five columns in the page, which stands for the number of the entry, the sRNA sequence name, mRNA sequence name, score and mRNA annotation, respectively. The prediction results are sorted in descending of scores. The prediction results can be displayed as text or downloaded as a compressed file.
Figure 1. The web interface for prediction of sRNA targets.
Figure 2. Demonstration of the prediction results.