With DNAMAN, you can compare two DNA sequences or two protein sequences in a dot matrix
plot. There are two methods for comparison. Method 1 uses a fast algorithm and is suitable
for long sequences. Method 2 performs progressive comparison to reduce the background of
low homology regions. The two methods yield different speed and accuracy in analysis.
DNAMAN displays the actual sequences and their alignment on any selected region in a
sequence window.
DNAMAN uses fast or optimal algorithms to align two DNA or protein sequences. You have
options to control the sensitivity of alignment. DNAMAN also allows you to select any
region of target sequences for alignment.
For DNA sequence alignment, you have an option to use the minus strand for comparison.
For protein sequence alignment, DNAMAN can report the amino acid similarity of two protein
sequences in a text window. The amino acid similarity matrix is editable by users.
