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

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Description

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

Usage

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extractProtPSSMFeature(pssmmat)

Arguments

pssmmat

The PSSM computed by extractProtPSSM.

Details

This function calculates the profile-based protein representation derived by PSSM. The feature vector is based on the PSSM computed by extractProtPSSM. 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 <http://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

extractProtPSSM extractProtPSSMAcc

Examples

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x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]

dbpath = tempfile('tempdb', fileext = '.fasta')
invisible(file.copy(from = system.file('protseq/Plasminogen.fasta', package = 'Rcpi'), to = dbpath))
pssmmat = extractProtPSSM(seq = x, database.path = dbpath)
pssmfeature = extractProtPSSMFeature(pssmmat)
head(pssmfeature)

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