※User Guide:

VIDEO GUIDE: VirusmapUserGuide.swf [Play][Download]


VirusMap is a visualization interface developed for the investigation of the epidemiological and geographical distribution in influenza A viruses. VirusMap contains an intact dataset of influenza A virus. In addition, a powerful analysis tool is also included. The tool is a workbench for phylogenetic analysis. This USAGE will introduce you to some of VirusMap's most commonly used components, including the visualization database and analysis tools.

1. Visualization Interface. In VirusMap, the main method for accessing the virus data is via the visualization interface. In the top left corner of the interface, various search options were implemented. You can select corresponding subtype, host, sampling time and/or sampling location to display the strains distribution. By clicking on the "Search" button, the geographical distribution pattern of the queried virus is displayed on Google Maps. For detail descriptions of the query results, please click on the marker or click the records included in the list provided on the left. By clicking on the "Statistics" button, a statistics page can be opened. From this statistics page, researchers may obtain a clear understanding of the overall distribution pattern.

2. The phylogenetic analysis workbench is a fully automated phylogenetic pipeline integrated BLAST (Camacho C et al., 2009), ClustalW (Larkin MA et al., 2007) and PHYLIP (Plotree D et al., 1998) packages. To perform a phylogenetic analysis, you should first enter your e-mail address. And then input your sequence in FASTA format. With the default setting, you can directly click on the "Submit" button to start a BLAST search. Significantly, you can click on the "Example" button to load an instance, which could help you to walk through the basic use of our workbench. A brief report containing homologous sequences will be shown after the BLAST search. Next, you just need to click on the "Build Tree" button and the analysis will be started automatically. When the calculation is completed, users immediately receive the result via e-mail.

Frequently Asked Questions:

1. Q: Can I save my search results for future use?

A: To save your search results, simply click on the "Browse" button. Then a summary page will show. In the first column of the summary page is the link to related NCBI page. From which you can download the full-length sequence. Again, you can save the summary page in HTML format via the save command in your browser.

2. Q: I can't open the website properly, what should I do?

A: We have tested VirusMap interface on several internet browsers, including Internet Explorer, Google chrome and Firefox. Please make sure you are using one of the above-mentioned browsers. In addition, if you can't view the marker properly, please close your firewalls. If your problem is still unresolved, please send us an email and tell us the OS information on your computer. We will resolve the problem ASAP.

3. Q: Why can't I receive the phylogenetic analysis results from VirusMap?

A: There could be several reasons why you can't receive your results. Please review the following situations to see if one applies to you: Did you enter a valid e-mail address? Please carefully check out your input so that the workbench can deliver your results properly. Did your e-mail server refuse to receive our message? In consideration of system safety, some SMTP servers will refuse to receive e-mails from specific domain name. Please try to use the e-mail services from Gmail, Hotmail or Yahoo. The above-mentioned e-mail addresses are well supported by our system.

4. Q: I have a few questions which are not listed above, how can I contact the authors of VirusMap?

A: Please contact the two major authors: Dr. Jian Ren, and Yubin Xie for details.