mcbasc {Bios2cor}

McBASC (McLachlan Based Substitution Correlation) function

Description

Calculates a score for each pair of residus in the sequenec alignment. It relies on a substitution matrix giving a similarity score for each pair of amino acids.

Usage

  mcbasc(align, gap_ratio= 0.2)

Arguments

align

An object of class 'align' created by the import.msf or the import.fasta function from a sequence alignment

gap_ratio

Numeric value between 0 and 1 indicating the maximal gap ratio at a given position in the MSA for this position to be taken into account. Default is 0.2, positions with more than 20 percent of gaps will not be taken into account in the analysis. When gap_ratio is 1 or close to 1, only positions with at least 1 aa are taken into account (positions with only gaps are excluded).

Details

The McBASC score at position [i,j] has been computed with a formula which was initially proposed by Valencia and coworkers(1) as follow :

{McBASC(i,j)} = \frac{1}{N^2\sigma(i)\sigma(j)} \sum_{k,l}^{ } (SC_{k,l}(i)-SC(i))(SC_{k,l}(j)-SC(j))

where :

• SC_{k,l}(i) is the score for the amino acid pair present in sequences k and l at position i

• SC_{k,l}(j) is the score for the amino acid pair present in sequences k and l at position j

• SC(i) is the average of all the scores SC_{k,l}(i)

• SC(j) is the average of all the scores SC_{k,l}(j)

• \sigma(i) is the standard deviation of all the scores SC_{k,l}(i)

• \sigma(j) is the standard deviation of all the scores SC_{k,l}(j)

Value

A list of two elements which are numeric matrices containing the mcbasc scores and Z-scores for each pair of elements.

Author(s)

Madeline DENIAUD and Marie CHABBERT

References

(1) Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18:309-317.

Examples

  #Importing MSA file
  align <- import.msf(system.file("msa/toy_align.msf", package = "Bios2cor"))

  #Creating correlation object with McBASC method for positions with gap_ratio < 0.2 (Default)
  mcbasc <- mcbasc(align, gap_ratio = 0.2)