get_seq_weights {BALCONY}R Documentation

Get sequences weights

Description

This function returns weights of the sequneces in the alignment object

Usage

get_seq_weights(alignment)

Arguments

alignment

alignment loaded with read.alignment

Details

The weights are calculated as shown in: Valdar and Thronton (2001)

According to the following formulas:

Wj = (∑ Dist(sj,sk))/N-1


where:
Wj is the weight of sequence sj, and is defined as the average evolutionary distance between sj and all other sequences in the alignment
N is the number of sequences in the alignment.

Dist(sj,sk)) = 1 = {∑ Mut(sj,sk)/n(Alignedjk))}

where:
Dist(sj,sk), the evolutionary distance between sequences sj and sk
Alignedjk is the set of all non-gap positions in sj or sk, n(Alignedjk) is the number of such positions.

Mut(a,b) = (m(a,b) - min(m))/(max(m) - min(m))

where:
Mut(a,b) measures the similarity between amino acids a and b as derived from a mutation data matrix m

Value

A vector with weights of length equal to the number of sequences in the alignment

Author(s)

Michal Stolarczyk & Alicja Pluciennik

References

Valdar, W. S. J. & Thornton, J. M. Protein–protein interfaces: Analysis of amino acid conservation in homodimers. Proteins: Structure, Function, and Bioinformatics 42, 108–124 (2001).

Examples

data("small_alignment")
alignment = small_alignment
weights = get_seq_weights(alignment)

[Package BALCONY version 0.2.10 Index]