Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

BMC Bioinformatics

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.

ISSN: 1471-2105