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 2.18.1 Index]