AA_REDUCED: Reduced amino acid alphabets

Description Usage Details References See Also Examples

Description

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

Usage

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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

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DECIPHER documentation built on Nov. 1, 2018, 4:42 a.m.