Identity Matrix
The simplest possible substitution matrix would be one in which each amino acid is considered maximally similar to itself, but not able to transform into any other amino acid. This matrix would look like:
This identity matrix will succeed in the alignment of very similar amino acid sequences but will be miserable at aligning two distantly related sequences. We need to figure out all the probabilities in a more rigorous fashion. It turns out that an empirical examination of previously aligned sequences works best.
Read more about this topic: Substitution Matrix
Famous quotes containing the words identity and/or matrix:
“Though your views are in straight antagonism to theirs, assume an identity of sentiment, assume that you are saying precisely that which all think, and in the flow of wit and love roll out your paradoxes in solid column, with not the infirmity of a doubt.”
—Ralph Waldo Emerson (1803–1882)
““The matrix is God?”
“In a manner of speaking, although it would be more accurate ... to say that the matrix has a God, since this being’s omniscience and omnipotence are assumed to be limited to the matrix.”
“If it has limits, it isn’t omnipotent.”
“Exactly.... Cyberspace exists, insofar as it can be said to exist, by virtue of human agency.””
—William Gibson (b. 1948)