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Table 1 Simulation parameters

From: Factors important in evolutionary shaping of immunoglobulin gene loci

Parameter

Description

Default value

Range

Basic Parameters

   

Generations:

The number of generations in the simulation

20000

 

Population size:

The number of organisms in the simulation

100

10-100

Segment length:

The number of bits in a gene segment string and in an antigen string

128

128, 512,1024

Maximum number of segments:

The upper limit on the size of an individual's genome library

250

50-250

Binding threshold:

The minimum binding affinity between antigen and antibody that is needed for protecting the individual from the antigen

0.53

0.3-0.7

Antigen number:

The antigen library size created in every generation

100

10-1000

Phenotype/Genotype ratio

The ratio between the number of antibody segments expressed in the phenotype and their number in the genome

0.2

0.1-1

Penalty function:

Penalty added to an organism's fitness as a function of genome size

fitness/(1 + tan(Ï€*n/(2*nmax))

where n is the number of segments in the organism's library and nmax is the maximum number of segments allowed.

Mutations Rates

All rates are in units of events/gene/generation, except the point mutation and bit deletion rates, which are in units of events/bit/generation.

Point mutation

The probability for every bit in every segment to change its value.

0.001

0.001 -0.014

Duplication

The probability of every segment to be duplicated

0.001

0.001 -0.014

Deletion

The probability of every segment to be deleted

0.001

0.001 -0.014

Exchange

The probability of a segment to swap its location with other randomly chosen segment.

0.001

0.001 -0.014

Inversion

The probability of a segment to change its orientation in the genome

0.001

0.001 -0.014

Bit deletion

The probability for every bit in every segment to be deleted

0.001

0.001 -0.014

  1. The parameters used in the simulation and their default values. For value justification see text.