entropy: Entropy score

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Entropy score

Description

Measures the entropy score of each position in a sequence alignment

Usage

  entropy(align, gap_ratio=0.2)

Arguments

align

An object created by the import.msf or the import.fasta function from a multiple sequence alignment file

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. 1 is excluded (positions with gaps only). 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 entropy score S at position i has been computed with a formula derived from the Shannon's entropy as follow :

{S(i)} = - \sum_{x}^{ } {p} _{x}(i) \log_{20} {p} _{x}(i)

where :

• i is the position in the sequence

• x is the sequence index

• {p} _{x}(i) represents the frequency of residue x at position i

Value

A vector containing an entropy value for each position in the alignment

Author(s)

Antoine GARNIER and Marie CHABBERT

References

Shannon CE. A mathematical theory of communication. Bell Syst Techn J 1948;27:379-423.

Examples

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

  #creating entropy object for positions with gap ratio < 0.5
  entropy <- entropy(align,gap_ratio=0.5)

Bios2cor documentation built on April 4, 2025, 4:14 a.m.