AA_REDUCED {DECIPHER} | R Documentation

## Reduced amino acid alphabets

### Description

The `AA_REDUCED` list contains reductions of the standard amino acid alphabet (`AA_STANDARD`).

### Usage

    AA_REDUCED

### Details

Reduced amino alphabets can sometimes improve sensitivity and specificity of finding homologous matches between amino acid sequences. The first twelve `AA_REDUCED` alphabets were optimized for finding synteny between genomic sequences. The next 113 alphabets are from a review of published amino acid alphabets (Solis, 2015). The final 17 alphabets were optimized for amino acid classification.

### References

Solis, A. (2015). Amino acid alphabet reduction preserves fold information contained in contact interactions in proteins. Proteins: Structure, Function, and Genetics, 83(12), 2198-2216.

### See Also

`FindSynteny`, `LearnTaxa`

### Examples

    str(AA_REDUCED)
    AA_REDUCED[[1]]

[Package DECIPHER version 2.20.0 Index]