CD-HIT-EST alignment parameters
<< CD-HIT analysis
<< Comparing USEARCH and CD-HIT
CD-HIT-EST alignment parameters
The default nucleotide alignment
parameters used by CD-HIT-EST, USEARCH and BLASTN are shown in the
table below. The CD-HIT (scaled) column gives equivalent values scaled
to a match score of +1, as used by the other programs.
| Parameter | CD-HIT | CD-HIT (scaled) | BLASTN | USEARCH |
| Match score | +2 | +1 | +1 | +1 |
| Mismatch score | -2 | -1 | -2 | -2 |
| Internal gap open penalty | 6 | 3 | 5 | 10 |
| End gap open penalty | 0 | 0 | n/a | 0.5 |
| Gap extend penalty | 1 | 0.5 | 2 | 0.5 |
Compared to BLASTN and USEARCH, the CD-HIT gap open penalty is lower and this tends to result in gappier alignments and higher sequence identities.
Examples
Gappy CD-HIT alignment that has 98% id according to CD-HIT but
95% id according to USEARCH.
Gappy CD-HIT alignment that has 86% id according to CD-HIT but 86% according to USEARCH.
Gross misalignment due to CD-HIT's use of banded dynamic programming.
These parameters apply to CD-HIT v4
through at least v4.5.7.
