For the convenience of the vast majority of experimental scientists, a step-by-step guide on how to use the Pse-in-One web server to get their desired results without the need to follow the complicated mathematic equations is given below.
Visit the web-server by clicking the link at http://bliulab.net/Pse-in-One/server and you will see the page as shown in Fig. 1. The three figures represent three sub web servers: PseDAC-General, PseRAC-General, and PseAAC-General for calculating the modes of DNA, RNA, and protein sequences, respectively.
Fig. 1
For DNA sequences
Step 1. If you click the first picture (DNA sequences) as shown in Fig. 1, then you will see the PseDAC-General web server (Fig. 2).
Fig. 2
Step 2. After you select one mode from the 14 modes listed in the pull-down menu in the Mode row, its corresponding parameters will be shown. You can click the “?” for the help information of various modes and their parameters. For example, if you select the PseKNC mode, you will see the page as shown in Fig. 2. You can either type or copy and paste the query DNA sequences into the input box or directly upload your input data by clicking the Choose File button. The input sequences should be in the FASTA format. You can just click the button Example to input the built-in sequence examples with default parameter setting as shown by Fig. 3.
Fig.3
Step 3. If you just click the button Example in the Step 2, and then click the Submit button, you will see a top page as shown in Fig.4. You can click the Download button to download the feature vectors in a text file. The distribution of the sequence composition values in the feature vector can be visualized by clicking the Visualization button and then you will see a heatmap as shown in Fig.5.
Fig. 4
Fig. 5
Step 1. If you click the second picture (RNA sequences) as shown in Fig. 1, then you will see the PseRAC-General web server as shown in Fig. 6.
Fig. 6
Step 2. After you select one mode from the 6 modes listed in the pull-down menu in the Mode row, its corresponding parameters will be shown. You can click the “?” for the help information of various modes and their parameters. For example, if you select the DACC mode, you will see the page as shown in Fig. 7. Then you can choose the physicochemical properties from followings for further calculations. Or you can upload a physicochemical index file defined by yourself. You can either type or copy and paste the query RNA sequences into the input box or directly upload your input data by clicking the Choose File button. The input sequences should be in the FASTA format. You can just click the button Example to input the built-in sequence examples with default parameter setting as shown by Fig.8.
Fig.7
Fig. 8
Step 3. If you click the button Example in the Step 2, and then click the Submit button, you will see a top page as shown in Fig.9. You can click the Download button to download the feature vectors in a text file. The distribution of the sequence composition values in the feature vector can be visualized by clicking the Visualization button and then you will see a heatmap as shown in Fig.10.
Fig.9
Fig.10
For protein sequences
Step 1. If you click the third picture (Protein sequences) as shown in Fig. 1, then you will see the PseAAC-General web server as shown in Fig.11.
Fig.11
Step 2. After you select one mode from the 8 modes listed in the pull-down menu in the Mode row, its corresponding parameters will be shown. You can click the “?” for the help information of various modes and their parameters. For example, if you select the Kmer mode, you will see the page as shown in Fig. 11. You can either type or copy and paste the query DNA sequences into the input box or directly upload your input data by clicking the Choose File button. The input sequences should be in the FASTA format. You can just click the button Example to input the built-in sequence examples with default parameter setting as shown by Fig. 12.
Fig. 12
Step 3. If you click the button Example in the Step 2, and then click the Submit button, you will see a top page as shown in Fig. 13. You can click the Download button to download the feature vectors in a text file. The distribution of the sequence composition values in the feature vector can be visualized by clicking the Visualization button and then you will see a heatmap as shown in Fig. 14.
Fig. 13
Fig. 14
