Abstract: Background: Dialign is a DNA/Protein alignment tool
for performing pairwise and multiple pairwise alignments through the
comparison of gap-free segments (fragments) between sequence
pairs. An alignment of two sequences is a chain of fragments, i.e
local gap-free pairwise alignments, with the highest total score.
METHOD: A new approach is defined in this article which relies on
the concept of using three-dimensional fragments – i.e. local threeway
alignments -- in the alignment process instead of twodimensional
ones. These three-dimensional fragments are gap-free
alignments constituting of equal-length segments belonging to three
distinct sequences. RESULTS: The obtained results showed good
improvments over the performance of DIALIGN.