HON-NEW Application

The HON-NEW application is a cool tool for figuring out the conservative and radical nonsynonymous distances between protein-coding DNA sequences. This method has been tweaked from the original approach by Hughes, Ota, and Nei in 1990, making it more accurate by considering transition bias.

Amino Acid Classifications

With HON-NEW, you get three different ways to classify amino acids: by charge, polarity, and based on Miyata and Yasunaga's method. Plus, you're not stuck with just these options—you can define your own conservative and radical amino acid changes!

Defining Amino Acid Groups

You can create groups of amino acids where changes between different groups are considered radical, while changes within the same group are seen as conservative. To set this up, just make a file called self.div.

How to Create Your Group File

In your self.div file, start with the first line listing the groups of amino acids. For example, if you're classifying by charge, you might have three groups: [-, 0, +]. On the second line, write down how many amino acids are in the first group followed by a space and then list those amino acids.

Amino Acid Codes

Remember to use the one-letter codes for each amino acid! After that line for the first group, you'll add information about the second group on the next line. You only need to include details for the first n-1 groups if you have n total groups because HON-NEW will figure out what’s in that last group from what you provided earlier.

If you're ready to dive into using this software or need more info on how it works, check out this link!