Definition of sequence identity
Identity and clustering
USEARCH uses the BLAST definition of identity, which is the
number of identities divided by the number of alignment columns. This is the
definition used by most bioinformatics programs.
See -id option for rules that
determine when a pair of letters match.
With a global alignment,
columns containing terminal gaps are discarded
before calculating identity. Internal gaps always count as
Different programs may report different
identities for the same sequences
The pair-wise identity between two sequences depends on the alignment and
the definition of identity. Alignments vary due to the use of different
parameters such as gap penalties and substitution scores. Definitions of
identity used by different programs may vary depending on the treatment of gaps
and detailed rules for deciding whether letters match (e.g., upper- and
lower-case and wildcards).
USEARCH, BLAST and CD-HIT definitions of %id
"identity" is a column with two matching letters.
USEARCH and BLAST = Identities / Columns
CD-HIT = Identities / (Length of shorter sequence)
Problems with the CD-HIT definition
For historical reasons, versions 5 and earlier of USEARCH used the CD-HIT
definition of identity. In versions 6 and later, the BLAST definition is used. I
made the change because I felt the CD-HIT definition had several important
weaknesses. The CD-HIT definition is not symmetrical between the longer and
shorter sequence. Gaps in the longer sequence reduce %id but gaps in the shorter
sequence do not. Gappier alignments therefore tend to have higher identities
according to CD-HIT compared to other methods, and the CD-HIT %id correlates
less well with evolutionary distance. A measure of %id that counts gaps as
differences is more robust against the choice of alignment parameters (gap
penalties and substitution matrices).
CD-HIT id is 97% and USEARCH id is 86%
CD-HIT id is 97% and USEARCH id is 95%