It says,
The Identity: is the percentage of identical matches between the two sequences over the reported aligned region (including any gaps in the length).
The Similarity: is the percentage of matches between the two sequences over the reported aligned region (including any gaps in the length).
here: http://embossgui.sourceforge.net/demo/manual/needle.html
So it's percentage of matches v. percentage of identical matches.
What is the difference?
2 answers
A match is defined as two aligned residues with a score above a threshold (here threshold is 1, they are indicated by : in the output, see the markup line description) so they can be different but having a high score means they are considered similar. Identity is only concerned with whether the two aligned residues are exactly the same regardless of score.
Thanks! That really clarifies it for me.
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