Figure 4. The Average Run Time.

(A) Time requirements as a function of λ. The “real data” curves were made using a SRP dataset. It contains eight pairs of 1,000 nucleotide-long sequences. Each sequence contains one SRP gene with a length of approximately 300 nucleotides. The “shuffled data” curve was made using shuffled versions of the same dataset. The “2.0” curves were made using the previous version of the program. “No pruning” curves were made using the current version, but without pruning (option -no_pruning). “Pruning” curves were made using the current version and default values of pruning. It is clear that the time needed to make the alignments explodes when pruning is not used, whereas the run time remains much lower when pruning is used.

(B) The pruning curves with a smaller time scale. The curve for the sequences containing a motif grows much faster than the curves for the shuffled sequences until the point where λ is as long as the motif. After this, the curves appear to grow at the same rate.