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Table 2 Run-time of each comparative method on the IRES_Picorna family of length 253 nt in the test set of simulated short genomes

From: Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

Method

# of processors used

Time (s)

Memory (MB)

DotcodeR

1

6.00

4.46

RNApdist

1

144.55

4.60

  1. Note that these results are only from real-against-real window comparison. The best performance is shown in bold face. This test was serially done on a server with Intel Xeon CPU 2.00 GHz with 8 cores and 65 GB memory
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BMC Genomics

ISSN: 1471-2164

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