Protein Remote Homology Detection by Combining PageRank and Hyperlink-Induced Topic Search

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Tutorial of HITS-PR-HHblits

HITS-PR-HHblits web server is constructed based on SCOPe v2.06, which is compatible with most major browsers. 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 HITS-PR-HHblits web server is given below.

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

HITS-PR-HHblits web-server
Figure 1. HITS-PR-HHblits web server

STEP 1: Input the query protein sequences

You can directly enter/paste the query protein 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 amino acids data. You can click the Examples button to automatically input the built-in sequence examples as shown in Fig 2, and click the Reset button to empty all input sequences.

Figure 2. The built-in example proteins

STEP 2: Submit your queries

If you enter query protein 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.

Figure 3. The processing page

STEP 3: 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 click the query IDs to view their corresponding results. For each query, their homologous proteins are listed in a table. Some useful sequence and structure information are provided, including SCOP ID, family classification, sequence length. You can find the protein primary sequence by click the 3D Structure button in Sequence column of the table.

Figure 4. The result page


Bin Liu
School of Computer Science and Technology, Beijing Institute of Technology, China.

Copyright@ By Liu Lab, Beijing Institute of Technology.

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