JFreq

Java Word Frequencies

Java Word Frequencies (JFreq) is a front end to Schbath’s R’MES, which is available at the R’MES website. R’MES finds the expected and actual frequencies of short nucleotide sequences, or words, using a Markov model to control for the effects of base composition and the frequencies of shorter words. Unusually frequent or infrequent occurrences of certain words may indicate biological relevance. For example, if the word “TAATTT” occurs much less frequently than expected, it might be that it performs some regulatory function, or makes the sequence vulnerable to mutation, or has some other biological function.

R’MES can also determine whether words occur in overlapping positions unusually often or unusually rarely, and the expected and actual frequencies of user-supplied words.

Sequences for analysis may be retrieved from the VOCs database, or loaded from a local file.

Getting Started

If you’re new to JFreq, 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 JFreq:

• 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.

Troubleshooting

If your system does not launch Viral Orthologous Clusters, it is probably missing Java Runtime Environment 1.5. Please see Java Web Start Setup and Java Web Start Tips for help.

Submit a feature request

Is there a feature that you think this tool needs? Submit a wish.