Laboratory of Bioinformatics 1 Flashcards
what is a PAM matrix?
amino-acid substitution matrix for studying protein evolution and sequences relationship. PAM stands for point accepted mutation (also referred to as percent accepted mutation) because it represents accepted point mutation per 100 amino acid residues.
A PAM represents a substitu-
tion of one amino acid by another that has been fixed
by natural selection because either it does not alter the
IN GENOMIC DATABASES: BLAST AND FASTA
protein function or it is beneficial to the organism.
In a PAM1 matrix, which is the original PAM matrix
generated, a PAM unit is an evolutionary time over which 1% of the amino acids in a sequence are expected to undergo accepted mutations, resulting in 1% sequence divergence.
The relationship between % amino acid substitution
and the number of PAM units is not linear; thus,
the above definition applies only when the divergence
between two sequences is low. As the divergence
increases beyond B20%, this relationship falls apart.
For example, a 100-PAM-unit divergence does not
mean 100% substitution. A 100-PAM-unit divergence
can be achieved by substituting B55% of the amino
acid residues, and a 200-PAM-unit divergence can be
achieved by substituting B75% of the amino acid resi-
dues. The PAM1 matrix was built by aligning closely
related protein sequences (71 protein families) that had
at least 85% sequence identity.
For example, the PAM250 matrix can be obtained by
multiplying the PAM1 matrix by itself 250 times over.
Figure 6.9 shows the PAM250 substitution matrix. The
values in the matrix are log odds scores.
Each PAM matrix is designed to be used for com-
paring sequences that are evolutionarily diverged by a
specific number of PAM units—that is, by a specific
length of evolutionary time. The suffix (number) with
PAM indicates evolutionary distance; the greater the
number, the greater is the distance.
what is bioinformatics
Bioinformatics is the development of computational
methods for studying the structure, function, and evolution of genes, proteins and whole genomes;
what is dynamic programming?
Dynamic programming is a method for solving complex problems by breaking them down into simpler subproblems.
what is a SCORING MATRIX?
A scoring matrix is a set of values representing the likelihood of one residue being substituted by another during sequence divergence through evolution. This is why the scoring matrix is also known as the substitution
matrix.
