Skip to main content

Table 3 Dynalign calculation time and memory requirements.

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

     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)
  1. 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.