Anchored and non-anchored alignment of a set of protein sequences with known 3D structure (data set lr69 from BAliBASE ). Three core blocks for which the 'correct' alignment is known are shown in red, blue and green. (A) Alignment calculated by DIALIGN with default options. Most of the core blocks are mis-aligned. (B) Alignment calculated by DIALIGN with anchoring option. The first position of the third block has been used as anchor point, i.e. the program has been forced to align this column correctly. The rest of the sequences is automatically aligned by DIALIGN given the constraints defined by this anchor point. Although only one single column has been used for anchoring, the tree blocks are almost perfectly aligned.