Difference between revisions of "Team:Heidelberg/internal tools"
(Corrected warnings about mutation rates and probabilties > 1.) |
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| Line 630: | Line 630: | ||
if(mr>1){ | if(mr>1){ | ||
| − | warnings += "A mutation rate that is above one mutation per basepair, per generation does not make sense. "; | + | warnings += "A mutation rate that is above one mutation per basepair, per generation does not make sense. 100 % should be enough, right? "; |
| + | mr = 1; | ||
} | } | ||
if(pm>1){ | if(pm>1){ | ||
| − | warnings +="A probability | + | warnings +="A probability of 100 % should be enough, right?. "; |
| − | + | pm = 1; | |
| − | + | ||
| − | + | ||
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| − | + | ||
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} | } | ||
| Line 680: | Line 672: | ||
$("#number_generations").html(ng_out); | $("#number_generations").html(ng_out); | ||
$("#number_to_seq").html(number_to_seq_out); | $("#number_to_seq").html(number_to_seq_out); | ||
| − | $("warnings_mutations").html( | + | $("#warnings_mutations").html(warnings); |
Revision as of 15:50, 21 September 2017
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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
