makowski: Diversity index according to Makowski

In peptider: Evaluation of Diversity in Nucleotide Libraries

Description

The Diversity of a peptide library of length k according to Makowski and colleagues

Usage

makowski(k, libscheme)

Arguments

k	length of peptide sequences
libscheme	Name (character vector) or definition (data frame) of scheme

Details

Makowski and colleagues [Makowski, Soares 2003] present another approach by defining functional diversity. They provide the mathematical background to determine the quality of a peptide library based on the probability of individual peptides to appear. In an ideal case, where every peptide has the same frequency the functional diversity is at a maximum of 1. With increasingly skew distributions, this value drops towards a minimum of 0. It is mostly independent of the actual number of sequences in a library but reflects effects caused by the degeneration of the genetic code. In the genetic code the number of codons per amino acid varies from one to six. Therefore random DNA sequences are biased towards encoding peptides enriched in amino acids encoded more frequently, which results in skew distributions of peptide frequencies.

Value

diversity index between 0 and 1

Examples

makowski(2, "NNN")
makowski(3, "NNK")
makowski(3, "2020")

peptider documentation built on May 2, 2019, 2:43 a.m.