From what I read, the sequences
AACTG
AACTGAC
have 100% identity, while the sequences
AACTG
AACTC
have 80% identity. What about
AATCG--C
AATCGAAC
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written
by
n00514450 •
There are many ways to calculate percent identity. Some take every character in a DNA string and compare it to another, whereas others explicitly exclude gapped or ambiguous sites. In your third case, the % identity depends on whether or not you include the sites that are gapped in the first sequence.
For a very short yet good synopsis, I recommend this paper by Alex May, "Percent Sequence Identity: The Need to be Explicit."
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written
by
Brice Sarver
Thank you. I guess the best thing to do is just ask my professor how he defines it.
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I like to use (#matches)/(alignment length), where alignment length includes gaps, because it is symmetric; you get the same identity regardless of which is the query and which is the reference. I count an N as 0.25 matches.
In practice, identity is often not a good metric, because it either gives exaggeratedly low scores to sequences with long indels, or ignores indels completely, neither of which makes much sense.