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Team:Edinburgh/Genetic Instability
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Revision as of 22:23, 18 July 2011
Ok, so apparently there exists this thing called genetic instability, and we need to counter it...
Contents |
What is genetic instability?
Genetic instability refers to the random reactions affecting DNA. When a lot of similar sequences of DNA are introduced to a cell, this can potentially lead to fragments of DNA re-arranging in an uncontrolled manner.
But there is a solution!
If we only had many different (as far apart as possible) DNA sequences coding for the same protein, the world would be saved!
Enter Team Synergy's genetic stability tool! It will do exactly that - using DNA's natural property of redundancy, it will find a number of sequences of DNA for you! And they will code for the same protein! Superb!
So, how does it work?
Possible modes
Random generation
This is a very crude mode, in which a random sequence of codons coding for analogous amino acids is generated, e.g. if you had:
atgaaaaagtctttagtcctcaaagcctctgtagccgttgctaccctcgttccgatgctgtctttcgct...
(the leader sequence for pVIII),
the program would translate it to amino acids sequence, i.e.:
MKKSLVLKASVAVATLVPMLSFA...
and then find a random codon for each amino acid, put them together, and spit out the result.
This sound too easy to be right... that's right!
Best codon
In this mode, the tool would choose the best codon per every amino acid. What is 'best codon'? It's the codon which has the most base pairs different from the original one.
For example, Leucine can be coded by UUA, UUG, CUU, CUC, CUA, or CUG. If the original sequence uses UUA, then the best codon method would choose CUU, CUC or CUG. Yeaaaah... . There often are plenty of 'best' codons, so this method would be improved if it looked at the wider context...
Genetic Algorithm
This is a very powerful algorithm
