Table 3.

Dynalign calculation time and memory requirements.

				Dynalign before acceleration			Dynalign after acceleration
System	Sequence 1	Sequence 2	Length (nt)	M	Time (hr:min)	Memory (MB)	M	Time (hr:min)	Memory (MB)
tRNA	RD0260	RE6781	77	15	0:22 (0:24)	33 (57)	6	0:01 (0:01)	12 (24)
5S rRNA	H. volcanii	A. globiformis	122	15	1:11 (1:09)	76 (85)	6	0:03 (0:03)	21 (30)
R2 3' UTR RNA	D. takahashii	D. melanogaster	217	24	26:05	491	8	0:39 (0:35)	81 (104)

Calculation times and memory use are reported for a 3.2 GHz Intel Pentium 4 with 1 GB RAM running Red Hat Enterprise Linux using the gcc 3.2.3-42 compiler. In parentheses are time and memory requirements on a laptop with a 3.06 GHz Pentium 4 processor and 1 GB of RAM running Microsoft Windows XP Professional using the Microsoft C++ .NET 2002 compiler. For Linux, CPU time is reported; for Windows, wall time is reported. "Length" is length of the first sequence. Sequences are obtained from [76, 77, 85, 86]. Note that this is the time requirement including suboptimal secondary structure prediction. Slightly less than half the computer time is required to find only the lowest free energy common structure.