The PseUI Server is a web-based implementation of PseUI model – a machine learning approach for pseudouridine sites identification of three species, H.sapiens, S.cerevisiae, and M.musculus. The outputs of PseUI are easy to understand, and could be browsed online or downloaded for further study. The results obtained by PseUI on the benchmark datasets for different species indicate that the current predictor may become a useful high-throughput tool for predicting pseudouridine sites.

The PseUI model was developed by using support vector machine based on three different kinds of features including position specific nucleotide propensity (PSNP), nucleotide composition (NC), and Pseudo dinucleotide composition (PseDNC).

The PseUI server requires a modern web browser with JavaScript and cookies enabled. The following browsers have been throughly tested with PseUI:

• Mozilla Firefox, version 4 or above
• Chrome, version 5 or above
• Internet Explorer, versions 7, and 8 or above

The latest version of Firefox and Chrome is recommended for visualization.

Analysis Procedure

To predict the possible psedouridine sites, following the steps below:.

• Submit your FASTA sequence (red ‘3’ in the above figure). You can also click the example button (red ‘1’ in the above figure) to get an example.

• Select a species that you need to analyze (red ‘2’ in above figure). Currently, three species, H.sapiens, S.cerevisiae, and M.musculus, are supported for predicting pseudouridine sites.

• Click button ‘Submit’ to submit request to PseUI, or click ‘Clear’ button to clear all sequences (red ‘4’ in the above figure). The result will be shown in a new page.

• The submitted RNA sequence must be longer than 21 bp for H.sapiens and M.musculus or longer than 31 bp for S.cerevisiae in FASTA format.

• If there is no uridine residue in the submitted RNA sequence, the PseUI server will have no output.

• The submitted RNA sequence cannot contain any illegal character. All but A, U, C and G are illegal characters

• If you make above mistake, you will get prompt message or warning message in the download file.

If you submit the sequence from the example and choose species as H.sapiens, the output is shown as in the above figure. There are two rows to show the results: ‘Sequence’ and ‘Marker’ (red ‘2’ in the above figure). In the ‘sequence’ row, the original query sequence is displayed. In the ‘Marker’ row, the position that the nucleotide in the original query sequence that predicted for pseudouridine site is highlighted in blue color (red ‘3’ in the above figure). If you want to continue to predict other species or other sequence, please click ‘Go Back Front’ (red ‘4’ in the above figure) button to return to the homepage.

If you want to download the predicted results, the ‘download’ button can be found in red ‘1’ in the figure of Results section. There is more detailed information that predicted to be the pseudouridine site. The above figure shows the predicted results for the sequence from the example, the first red box (red ‘1’ in the above figure) indicates the location of pseudouridine sites in the whole query sequence, and the second red box (red ‘2’ in the above figure) represents the serial number of the query sequence.

If you have any suggestion or problem about PseUI server , please send us email directly.