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

This function calculates the profile-based protein representation derived by PSSM. The feature vector is based on the PSSM computed by extractPSSM.

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

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.

Author

Nan Xiao <https://nanx.me>

Examples

if (Sys.which("makeblastdb") == "" | Sys.which("psiblast") == "") {
  cat("Cannot find makeblastdb or psiblast. Please install NCBI Blast+")
} 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)
}
#> Cannot find makeblastdb or psiblast. Please install NCBI Blast+