Point accepted mutation
Encyclopedia
Point accepted mutation is a set of matrices
used to score sequence alignment
s. The PAM matrices were introduced by Margaret Dayhoff in 1978 based on 1572 observed mutations in 71 families of closely related proteins. Each matrix has the twenty standard amino acids in its twenty rows and columns; the value in a given cell represents the probability of a substitution of one amino acid for another. This type of matrix is commonly known as a substitution matrix
.
This matrix is used to derive a scoring matrix, used in bioinformatics
to assess the similarity of two aligned sequences. For example, an 18% probability of replacing arginine with lysine (in the substitution matrix) is turned into a score of 3 in the scoring matrix. The calculation uses the ratio of the probability value and the frequency of the original amino acid (arginine) in known sequences.
The PAM matrices imply a Markov chain
model of protein mutation. The PAM matrices are normalized so that, for instance, the PAM1 matrix gives substitution probabilities for sequences that have experienced one point mutation
for every hundred amino acids. The mutations may overlap so that the sequences reflected in the PAM250 matrix have experienced 250 mutation events for every 100 amino acids, yet only 80 out of every 100 amino acids have been affected.
Matrix (mathematics)
In mathematics, a matrix is a rectangular array of numbers, symbols, or expressions. The individual items in a matrix are called its elements or entries. An example of a matrix with six elements isMatrices of the same size can be added or subtracted element by element...
used to score sequence alignment
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
s. The PAM matrices were introduced by Margaret Dayhoff in 1978 based on 1572 observed mutations in 71 families of closely related proteins. Each matrix has the twenty standard amino acids in its twenty rows and columns; the value in a given cell represents the probability of a substitution of one amino acid for another. This type of matrix is commonly known as a substitution matrix
Substitution matrix
In bioinformatics and evolutionary biology, a substitution matrix describes the rate at which one character in a sequence changes to other character states over time...
.
This matrix is used to derive a scoring matrix, used in bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
to assess the similarity of two aligned sequences. For example, an 18% probability of replacing arginine with lysine (in the substitution matrix) is turned into a score of 3 in the scoring matrix. The calculation uses the ratio of the probability value and the frequency of the original amino acid (arginine) in known sequences.
The PAM matrices imply a Markov chain
Markov chain
A Markov chain, named after Andrey Markov, is a mathematical system that undergoes transitions from one state to another, between a finite or countable number of possible states. It is a random process characterized as memoryless: the next state depends only on the current state and not on the...
model of protein mutation. The PAM matrices are normalized so that, for instance, the PAM1 matrix gives substitution probabilities for sequences that have experienced one point mutation
Point mutation
A point mutation, or single base substitution, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material, DNA or RNA. Often the term point mutation also includes insertions or deletions of a single base pair...
for every hundred amino acids. The mutations may overlap so that the sequences reflected in the PAM250 matrix have experienced 250 mutation events for every 100 amino acids, yet only 80 out of every 100 amino acids have been affected.