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

### 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. Proteinâ€“protein interfaces: Analysis of amino acid conservation in homodimers. Proteins: Structure, Function, and Bioinformatics 42, 108â€“124 (2001).

### Examples

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

[Package

*BALCONY* version 0.2.10

Index]