Running FluMap jobs involves three screens (steps) - input, review, and result. At each screen you are provided with help messages as popup buttons for major input parameters.

The input screen provides form fields required to run FluMap jobs. The main data are your Sequences (either by file upload or direct input) and Template file. Other parameters include: Virus Name, Score Type, and Color Scheme for visualizing conservation.


Sequences shall be provided by either file upload or direct input in the text field.

Sequences should be listed in FASTA format.


A PDB (Protein Data Bank) formatted file that holds the macromolecular structure data to be uploaded and used for the 3D display.


Virus Name: The name of the query sequence that the user wants to compare against the other query sequences.

Score Type: We provide six scoring methods in FluMap - ENTROPY, CHEM6, CHEM9, PAM250, BLOSUM62, and HOMOLOGY.

Color Scheme: We provide six color scheme options for visualizing conservation. Choose the best suitable one for your data.

Submit Input Form

Once you are ready, click to submit input form. Your input will be automatically checked. You will be prompted with a warning window if any of your input does not pass validation.

Once your input data have passed the initial validation, all parameters and input data will be presented on the second screen for review purpose.


Based on uploaded template PDB file, all its existing chains are listed. Please choose one chain for visualization.


Uploaded sequences are also listed on this screen. You can scroll left/right to review and double-check.

Review Data

If you do not think the input data are correct, you can click to go back to the first screen.
Otherwise, click to initiate FluMap computation job.

  • Depending on the size and complexity of your input data, as well as score type, a FluMap job may take longer time to run. Please be patient.
  • Once the computation job finishes, a 3D structured will be constructed using JSmol (a JavaScript version of Jmol). Since the final result is a 3D structure, it may also take a few seconds to load.
  • All menu options of JSmol can be initiated by positioning your mouse pointer inside JSmol drawing area and Right-Click.
  • You are also provided with exporting options on the result screen.
  • To view the alignment and Amino Acid conservation among uploaded sequences, we provide a Jalview button. Clicking on it will bring a separate window visualizing sequence alignment.