Description
Java Word Frequencies
Java Word Frequencies is a neat little tool that acts as a front end for Schbath's R'MES. This software helps you find how often certain short nucleotide sequences, or words, show up in your data.
Understanding R'MES
So, what exactly does R'MES do? It uses a Markov model to look at the expected and actual frequencies of these short sequences. It takes into account things like base composition and how often shorter sequences appear. Pretty cool, right?
Why Word Frequencies Matter
You might wonder why this matters. Well, if you notice that a certain word shows up way more or way less than you'd expect, it could mean something important biologically. For instance, if the sequence "TAATTT" pops up much less than you'd think, it might be doing something special—like regulating functions or making the sequence more prone to mutations.
Overlapping Positions
R'MES also has some extra tricks up its sleeve! It can check if words appear in overlapping positions more frequently or rarely than expected. Plus, you can input your own words and see their expected versus actual frequencies!
Get Started with Java Word Frequencies
If you're ready to dive into word frequency analysis, download Java Word Frequencies here!
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Java Word Frequencies is a powerful tool for analyzing nucleotide sequences to uncover biological relevance through word frequencies.