Alignment Evaluation: This is the final step of sequence alignment. By comparing the alignment of sequences and alignment of their 3D structures we can assess its accuracy. This is possible of course only when we are working with family of proteins for which the three dimensional structures are known at least for two proteins. If we include the tertiary structural features in the alignment it gives a set of test alignments against which sequence-only alignments can be compared. The sequences with unknown three dimensional structures of the family can apply the similar conditions. To extend this approach to the unknown structure, one should use protein structure prediction algorithms to recognize possible secondary structural elements.