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Table 2 The running times (in seconds) of different programs searching for various descriptors in the whole human genome

From: RNA motif search with data-driven element ordering

  ATP apt. GTP apt. generalized HHR-I HHR-II HHR HDV HDV HDV
   class I tRNA (4 bp) (3 bp) extended (loose P4) (stem P4) (mispairs)
RNAbob 3,419.03 2,744.30 7,450.07 923.53 5,027.33 2,269.35 209,932.57 43,430.78 36,459.87
RNAmotif 80.78 222.54 7,374.32 87.69 265.09 116.15 26,259.79 2,513.90 9,240.83
RNAMot unf unf unf unf unf unf unf 4,538.92 8,925.31
RNArobo 80.91 151.09 250.63 96.48 110.64 108.46 171.16 169.90 111.30
RNArobo-ins 153.38 98.22 137.47 173.82 171.54
  1. Experiments were run on Intel Xeon E5520 CPU. RNArobo-ins is RNArobo run with modified descriptors allowing insertions in helical elements. RNAMot did not finish on most of the inputs within time limit of three days. Only results that finished within three days are shown. Since DDEO is randomized, we show the average running time of five runs of RNArobo. Standard deviation was up to 3 % or 5 sec, with the exception of the HHR extended descriptor, where the running time ranged from 98 to 125 sec
  2. Boldface numbers represent the best running times for a particular descriptor