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(π*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 |