Comparison of transition seeds designed for noncoding HSPs. Each ROC curve shows seeds with the same transition weight m but different match weights w. The curve corresponding to BLASTZ seed starts with a seed with w = 11 and m = 1. All the other curves start with a seed with w + m/2 = 11. For each curve, the subsequent points decrease w by 1 while holding m constant. Each point represents a locally optimal set of seeds.