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)
“As all historians know, the past is a great darkness, and filled with echoes. Voices may reach us from it; but what they say to us is imbued with the obscurity of the matrix out of which they come; and try as we may, we cannot always decipher them precisely in the clearer light of our day.”
—Margaret Atwood (b. 1939)