Kimura-2 parameters

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Kimura-2-Parameter (K2P) is a method named after the Japanese scientist Motoo Kimura from 1980 for correcting distance data from a sequence alignment .

introduction

In order to construct a family tree, orthologous sequences of genome segments , mostly genes, are written below one another and "meaningfully" compared with one another (creation of a multiple sequence alignment ). From this you can then create family trees. There are 2 basic approaches for doing this. Either you compare each individual character ( amino acid for protein sequences or bases for DNA ) ( character-oriented family tree creation ) or you convert the individual places into so-called distance data . The distances between the characters are calculated and a matrix is ​​created from this, with which the sequences can be compared ( matrix-oriented family tree creation ).

Explanation

If you want to construct a molecular family tree and want to use a distance method, you have to correct the calculated distance data so as not to ignore reverse mutations. This is especially important with larger evolutionary distances.

In contrast to Jukes & Cantor , K2P takes into account the fact that transitions (exchange from purine base to purine base or exchange from pyrimidine base to pyrimidine base ) are more likely than transversions (exchange from purine base to pyrimidine base or vice versa ). So 2 parameters are considered (name!), Which has a decisive advantage over Jukes & Cantor.

Like Jukes & Cantor, K2P assumes that all bases in the sequence occur approximately equally.

literature