Difference between revisions of "Team:Heidelberg/internal tools"
(Bugfixes, warning about mutation rates > 1) |
|||
| Line 644: | Line 644: | ||
//calculate | //calculate | ||
if(phi*tt==0){ | if(phi*tt==0){ | ||
| − | a_mutations = | + | a_mutations = 1 - Math.pow((1 - mr), ng); |
ng_out = ""; | ng_out = ""; | ||
} | } | ||
else{ | else{ | ||
| − | a_mutations = mr | + | a_mutations = 1 - Math.pow((1 - mr), tt*phi); |
ng = tt*phi; | ng = tt*phi; | ||
ng_out = "The conditions result in " + ng + " generations." | ng_out = "The conditions result in " + ng + " generations." | ||
Revision as of 15:18, 21 September 2017
WikitemplateA home
From 2014.igem.org
Internal Tools
Number of mutations and mutated sequences
Expected number of mutations in a single sequence: $$p_{m} = \frac{N_{mutations}}{L_{Sequence}} = N_{generations} \cdot r_{mutation} = t_{total} \cdot \Phi \cdot r_{mutation}$$
The expected share of sequences that shows at least one mutation in \(L_{Sequence}\) bp is the probability that \(L_{sequence}\) basepairs stay unchanged when \(\frac{N_{mutations}}{L_{Sequence}}\) mutations are expected: $$p_{M} = \frac{N_{mutated}}{N_{Sequences}} = 1 - p(N_{mutations}=0) = 1 - (1-p_{m})^{L_{Sequence}} $$
With this equation we can also calculate the number of sequences \(N_{Sequences}\) that have to be sequenced in order to find a mutated one with a probability of \(p(N_{mutated} > 0)\). $$ N_{Sequences} = \frac{p(N_{mutated} > 0)}{p_{M}} $$
The probability to find at least one mutated sequence under the given conditions is $$p(N_{mutated}>0) = 1 - (1-p_{M})^{N_{sequences}}$$ which gives $$N_{Sequences} = \frac{ln(1-p(N_{mutated}>0))}{ln(1-p_{M})}$$
Set \(\Phi\) to zero to use the number of generations for the calculation. If \(\Phi\) and the number of generations are given, \(\Phi\) is used.
Consider \(L_{Sequence}\) as the number of basepairs that is expected to be mutated. If half of the sequence you are interested in, is highly conserved choose a lower \(L_{Sequence}\).
\(p_{m} =\) %(bp/bp).
\(N_{mutations} =\) bp per sequence.
The share of sequences that shows at least one mutation in \(L_{Sequence}\) bp is \(p_{M}=\) % of sequences
