identification of circRNA-disease associations based on Learning to Rank

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Tutorial of iCircDA-LTR web server

iCircDA-LTR web server is constructed to predict associated diseases for query circRNAs, which is compatible with most major browsers, and the parallel speed-up is implemented. It offers an open and interactive web service, which accepts query sequences in FASTA format and returns the search results in a user-friendly manner. For the convenience of the experimental scientists, a step-by-step guide on how to use the iCircDA-LTR web server is given below.

Visit the web server by clicking the link at http://bliulab.net/iCircDA-LTR/server and you will see the page as shown in Fig. 1. The Microsoft Edge and Google Chrome browsers are recommended.

iCircDA-LTR web server
Fig. 1.Web server of iCircDA-LTR

Step 1: Input the genomic sequences of query circRNAs

You can directly enter/paste the query circRNA sequences into the input box, or upload them via file by clicking the Choose File button. All the input sequences should be in the FASTA format. A sequence in FASTA format consists of a single line beginning with the symbol ">" and multiple lines of base sequence data. You can click the Examples button to automatically input the built-in sequence examples, as show in Fig. 2, and click the Reset button to empty all input sequences.

Fig. 2. The built-in example circRNAs

Step 2: Set the parameters

The LTR score cutoff is used for results output, and higher LTR score represents higher confidence. In addition, the Email address is optional, please input your valid Email address so that we can send the results to you.

Step 3: Submit your queries

If you enter query circRNA sequences, and then click the Submit button, you will see a processing page as shown in Fig. 3. Your job is being processed. The results will be shown on your screen when it is finished. You can also close this browser window, and reload the results by using the link.

Fig. 3. The processing page

Step 4: View results

The results will be shown on your screen when it is finished, as shown in Fig. 4. The results will be stored for 7 days, and you can click the Download link to download it. You can find the circRNA primary genomic sequence by clicking the circRNA button in Visualization column of the table. Corresponding predicted results can be download by clicking the corresponding download buttons in Visualization column of the table.

Fig. 4. The result page