Table 1 Total CPU time and alignment quality for DIALIGN (D) and DIALIGN anchored with CHAOS (C+D) applied to a set of 42 pairs of genomic sequences from human and mouse [12]. CHAOS was run with varying cutoff parameters. Lower cutoff values for CHAOS produced higher numbers of anchor points resulting in a decreased search space for the final DIALIGN alignment procedure thus leading to improved running time but slightly decreased alignment quality. The average number of anchor points per kilobase is shown (anc./kb). Score is the total numerical score of all produced DIALIGN alignments, i.e. the sum of the scores of the segment pairs in the alignments. As a rough measure of the biological quality of the produced alignments, we compared local sequence similarities identified by DIALIGN and CHAOS to known protein-coding regions. Here, Sn, Sp and AC are sensitivity, specificity and approximate correlation, respectively. For the D and C+D results, DIALIGN was evaluated by comparing all segment pairs contained in the alignment to annotated exons.

From: Fast and sensitive multiple alignment of large genomic sequences