Hydrophobicity
NOTE: This tool requires Java Version 8. Download it here: Java Runtime Environment.
Hydrophobicity Grapher
Hydrophobicity Grapher graphs the hydrophobicity/hydrophilicity of a sequence of amino acids, using a sliding window. The window size can be specified by the user, and several hydrophobicity scales can be used to determine the plot.
Because of how the plot is calculated, the very beginning and very end of the sequence will be cut off. The amount cut off will depend on the window size: exactly one half of the window size will be deleted from the beginning of the sequence, and the same amount will be cut off the end. Therefore, if one has a window size of 20, the first and last 10 amino acids will not be plotted.
Getting Started
If you’re new to Hydrophobicity Grapher, click on the launch button (on the right) and use the Quick Start Page to learn the basics (or if you’re like us… just start clicking!)
The VBRC also provides additional help resources for Hydrophobicity Grapher:
- How to doc; short descriptions of certain analyses you might want to do.
- FAQs (Frequently Asked Questions)
- Finally, just email us a question and we’ll gladly help you out.
References
Kyte J, Doolittle RF.
A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105-32.
Hopp TP, Woods KR.
A computer program for predicting protein antigenic determinants. Mol Immunol. 1983 Apr;20(4):483-9.
Parker JM, Guo D, Hodges RS.
New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry. 1986 Sep 23;25(19):5425-32.
Troubleshooting
If your system does not launch Viral Orthologous Clusters, it is probably missing Java Runtime Environment 1.8. Please see Java Web Start Setup and Java Web Start Tips for help.
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