extractPSSMFeature: Profile-based protein representation derived by PSSM...

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/desc-15-PSSMFeature.R

Description

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

Usage

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Arguments

pssmmat

The PSSM computed by extractPSSM.

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)).

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).

Author(s)

Nan Xiao <https://nanx.me>

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

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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)

}

protr documentation built on Nov. 18, 2017, 9:03 a.m.