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 remaining alphabets are from a review of published amino acid alphabets (Solis, 2015).

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

Examples

str(AA_REDUCED)
AA_REDUCED[[1]]

[Package DECIPHER version 2.8.1 Index]