BioMedR (version 1.2.1)

extrProtCTDCClass: CTD Descriptors - Composition (with Customized Amino Acid Classification Support)

Description

CTD Descriptors - Composition (with Customized Amino Acid Classification Support)

Usage

extrProtCTDCClass(x, aagroup1, aagroup2, aagroup3)

Arguments

x

A character vector, as the input protein sequence.

aagroup1

A named list which contains the first group of customized amino acid classification. See example below.

aagroup2

A named list which contains the second group of customized amino acid classification. See example below.

aagroup3

A named list which contains the third group of customized amino acid classification. See example below.

Value

A length k * 3 named vector, k is the number of amino acid properties used.

Details

This function calculates the Composition descriptor of the CTD descriptors, with customized amino acid classification support.

References

Inna Dubchak, Ilya Muchink, Stephen R. Holbrook and Sung-Hou Kim. Prediction of protein folding class using global description of amino acid sequence. Proceedings of the National Academy of Sciences. USA, 1995, 92, 8700-8704.

Inna Dubchak, Ilya Muchink, Christopher Mayor, Igor Dralyuk and Sung-Hou Kim. Recognition of a Protein Fold in the Context of the SCOP classification. Proteins: Structure, Function and Genetics, 1999, 35, 401-407.

See Also

See extrProtCTDTClass and extrProtCTDDClass for Transition and Distribution of the CTD descriptors with customized amino acid classification support.

Examples

# NOT RUN {
x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]

# using five customized amino acid property classification
group1 = list(hydrophobicity  = c('R', 'K', 'E', 'D', 'Q', 'N'),
              normwaalsvolume = c('G', 'A', 'S', 'T', 'P', 'D', 'C'),
              polarizability  = c('G', 'A', 'S', 'D', 'T'),
              secondarystruct = c('E', 'A', 'L', 'M', 'Q', 'K', 'R', 'H'),
              solventaccess   = c('A', 'L', 'F', 'C', 'G', 'I', 'V', 'W'))

group2 = list(hydrophobicity  = c('G', 'A', 'S', 'T', 'P', 'H', 'Y'),
              normwaalsvolume = c('N', 'V', 'E', 'Q', 'I', 'L'),
              polarizability  = c('C', 'P', 'N', 'V', 'E', 'Q', 'I', 'L'),
              secondarystruct = c('V', 'I', 'Y', 'C', 'W', 'F', 'T'),
              solventaccess   = c('R', 'K', 'Q', 'E', 'N', 'D'))

group3 = list(hydrophobicity  = c('C', 'L', 'V', 'I', 'M', 'F', 'W'),
              normwaalsvolume = c('M', 'H', 'K', 'F', 'R', 'Y', 'W'),
              polarizability  = c('K', 'M', 'H', 'F', 'R', 'Y', 'W'),
              secondarystruct = c('G', 'N', 'P', 'S', 'D'),
              solventaccess   = c('M', 'S', 'P', 'T', 'H', 'Y'))

extrProtCTDCClass(x, aagroup1 = group1, aagroup2 = group2, aagroup3 = group3)
# }