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Table 3 Resource Utilization Comparison.

From: Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

Sequence Pair CPU (sec) RAM (MB)
unconstrained pairSCFG
RD0260 vs RE6781 tRNAs 718 285
M16173 vs X02128 5S 22902 1465
constrained pairSCFG (post 0.95; W = 20)
RD0260 vs RE6781 tRNAs 31 64
M16173 vs X02128 5S 347 248
Dynalign ( MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBamrtHrhAL1wy0L2yHvtyaeHbnfgDOvwBHrxAJfwnaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaWaaeGaeaaakeaaimaacqWFZestaaa@3790@ = 15; gap = 0.4)
RD0260 vs RE6781 tRNAs 1761 33
M16173 vs X02128 5S 4928 67
Stemloc (-na 100 -nf 1000)
RD0260 vs RE6781 tRNAs 6 85
M16173 vs X02128 5S 18 193
PMcomp (-p -noLP for RNAfold)
RD0260 vs RE6781 tRNAs 19 52
M16173 vs X02128 5S 33 142
FOLDALIGN (-max_diff 25 -global -score_matrix global. fmat)
RD0260 vs RE6781 tRNAs 25 77
M16173 vs X02128 5S 87 280
  1. The resource requirements for a single representative tRNA and 5S sequence pair for each of the five constrained Sankoff implementations and the unconstrained pairSCFG Sankoff implementation, given as a baseline reference.
  2. The tRNA sequences are of length 78 and 77 respectively. The 5S sequences are of length 117 and 118 respectively. The constrained pairSCFG utilizes the pin selection criteria of posteriors > 0.95 and a protection window of 20. (For these examples the result is 2 pins for the tRNA pair and 3 pins for the 5S pair.) Dynalign is compared using the parameters recommended in [35] of MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBamrtHrhAL1wy0L2yHvtyaeHbnfgDOvwBHrxAJfwnaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaWaaeGaeaaakeaaimaacqWFZestaaa@3790@ = 15 and a gap penalty of 0.4 kcal mol-1 gap-1. Stemloc is compared using the parameters recommended in [31] which computes 100 alignment envelopes (-na 100) and 1000 fold envelopes (-nf 1000). For PMcomp, the reported time includes both calculating the pair probability (via RNAfold with parameters -p -noLP) and the subsequent phase. The memory reported is the maximum utilized during either phase. With FOLDALIGN, the parameters from Gardner are utilized (-max_diff 25-global -score_matrix global.fmat). For all programs these are the same parameters utilized to generate the performance reflected in Figure [7]. These benchmarks were conducted on a dual 2.8 GHz P4 machine with 2.5 GB memory running the Linux 2.4 kernel.