Description Usage Arguments Details Value Author(s) References Examples
This function returns weights of the sequneces in the alignment object
1 |
alignment |
alignment loaded with |
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
A vector with weights of length equal to the number of sequences in the alignment
Michal Stolarczyk & Alicja Pluciennik
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).
1 2 3 | data("small_alignment")
alignment = small_alignment
weights = get_seq_weights(alignment)
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