landgraf_conservativity {BALCONY}R Documentation

Calculate Landgraf conservation score

Description

This function calculates Landgraf conservarion score

Usage

landgraf_conservativity(matrix_name = NULL, alignment, weights)

Arguments

matrix_name

A string with path to the file woith substitution matrix to be used to calculate the Landgraf conservation score. Optional parameter, if not provided the Gonnet substitution matrix is used (according to author's suggestion)

alignment

An alignment object read with read.alignment function

weights

A vector with weight for each sequence in the alignment to be used to calculate the Landgraf conservation score e.g. each sequence similarity to the consensus sequence from the alignment - output from cons2seqs_ident fuction

Value

score

A vector of length equal to the length of aligned sequences

Note

Please note that the Shannon matric formula can be found in the paper listed in "See Also" section below. Also, this function originally calculates the entropy values which can be used to estimate the conservativity score according to the following formula:

conservation = 1 - entropy

Author(s)

Michal Stolarczyk & Alicja Pluciennik

See Also

consensus, cons2seqs_ident, read.alignment

http://onlinelibrary.wiley.com/doi/10.1002/prot.10146/abstract

Examples

data("small_alignment")
alignment = small_alignment
threshold_consensus = 30
consensus_seq=consensus(alignment, threshold_consensus);
consensus_sequences_identity=cons2seqs_ident(alignment, consensus_seq)
score = landgraf_conservativity(alignment = alignment, weights = consensus_sequences_identity)

[Package BALCONY version 0.2.10 Index]