protr (version 1.2-0)

extractPSSMFeature: Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)

Description

Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)

Usage

extractPSSMFeature(pssmmat)

Arguments

pssmmat

The PSSM computed by extractPSSM.

Value

A numeric vector which has 20 x N named elements, where N is the size of the window (number of rows of the PSSM).

Details

This function calculates the profile-based protein representation derived by PSSM. The feature vector is based on the PSSM computed by extractPSSM. For a given sequence, The PSSM feature represents the log-likelihood of the substitution of the 20 types of amino acids at that position in the sequence. Each PSSM feature value in the vector represents the degree of conservation of a given amino acid type. The value is normalized to interval (0, 1) by the transformation 1/(1+e^(-x)).

References

Ye, Xugang, Guoli Wang, and Stephen F. Altschul. "An assessment of substitution scores for protein profile-profile comparison." Bioinformatics 27.24 (2011): 3356--3363.

Rangwala, Huzefa, and George Karypis. "Profile-based direct kernels for remote homology detection and fold recognition." Bioinformatics 21.23 (2005): 4239--4247.

See Also

extractPSSM extractPSSMAcc

Examples

if (Sys.which('makeblastdb') == '' | Sys.which('psiblast') == '') {
  cat('Could not find makeblastdb or psiblast. Please install NCBI Blast+ first.')
} else {
  x = readFASTA(system.file('protseq/P00750.fasta', package = 'protr'))[[1]]
  dbpath = tempfile('tempdb', fileext = '.fasta')
  invisible(file.copy(from = system.file('protseq/Plasminogen.fasta',
                                         package = 'protr'), to = dbpath))
  pssmmat = extractPSSM(seq = x, database.path = dbpath)
  pssmfeature = extractPSSMFeature(pssmmat)
  head(pssmfeature)
}