### Table 1. Results of various algorithms on the Motif Challenge Problem

2003

"... In PAGE 4: ... This motivated the more powerful algorithms PRO- JECTION (Buhler and Tompa, 2001), MITRA (Eskin and Pevzner, 2002) and MULTIPROFILER (Keich and Pevzner, 2002a), which are able to solve much harder implantation problems. In Table1 , we list the success rate and running time of PatternBranching on the Motif Challenge Problem, versus each of these algorithms. We define success to mean that the algorithm outputs the implanted motif pattern.... ..."

### Table 10: Execution time on an SGI Power Challenge for algorithm [DSD].

### Table 12: Execution time on an SGI Power Challenge for algorithm [BSD].

### Table 13: Execution time on an SGI Power Challenge for algorithm [DSI].

### Table 15: Execution time on an SGI Power Challenge for algorithm [BSI].

### Table 16: Execution time on an SGI Power Challenge for algorithm [XSI].

### Table 8: Algorithm performance for the DIMACS set of coloring challenge graphs. Algorithm applied: lmXRLF.

### Table 2. Results of various profile-based algorithms on the Motif Challenge Problem

2003

### TABLE II ILLUSTRATION OF TRADEOFF BETWEEN PERFORMANCE AND RUNNING TIME OUR ALGORITHM ON THE CHALLENGE PROBLEM DATASET FOR THE (15;4) MOTIF. nfi IS SET TO 4 AND nfl IS INCREASED GRADUALLY.

### Table 9: Runtime(seconds)and speedups forparallel algorithm on SGI Power Challenge multiprocessorforhierarchical graphs

1996

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