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.

Uzilov et al. BMC Bioinformatics 2006 7:173   doi:10.1186/1471-2105-7-173