Skip to main content

Table 6 Comparison of three ncRNA detection programs on a whole genome screen using the MUMmer alignment.

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

  probability cutoff for ncRNA classification  
  P > 0.5 P > 0.9 P > 0.99  
  Dynalign RNAz Dynalign RNAz Dynalign RNAz QRNA
Known ncRNAs found (percent of total known ncRNAs in parentheses)
E. coli (156 ncRNAs known) 128 (82.05) 125 (80.13) 123 (78.85) 104 (66.67) 107 (68.59) 91 (58.33) 67 (42.95)
S. typhi (110 ncRNAs known) 103 (93.64) 98 (89.09) 102 (92.73) 84 (76.36) 93 (84.55) 70 (63.64) 64 (58.18)
Number of contiguous, non-overlapping hits that are not known ncRNAs (i.e. novel ncRNA candidates)
E. coli 1,183 1,255 872 996 578 678 661
S. typhi 1,178 1,255 857 977 568 662 634
Number of nucleotides classified as ncRNA that are not in known ncRNAs (i.e. nucleotides in novel ncRNA candidates)
E. coli (each strand = 4,639,675 nt) 169,580 174,790 123,563 128,343 81,936 80,054 87,577
S. typhi (each strand = 4,809,037 nt) 163,037 174,126 117,277 126,393 76,289 79,713 88,099
Total number of nucleotides classified as ncRNA (i.e. nucleotides in both known and unknown ncRNAs)
E. coli (each strand = 4,639,675 nt) 224,051 222,817 175,174 166,676 129,086 104,428 113,090
S. typhi (each strand = 4,809,037 nt) 213,549 218,867 166,187 162,077 122,269 102,464 114,434
  1. QRNA, RNAz, and the Dynalign/LIBSVM classifier are compared in their ability to detect known ncRNA in the E. coli and S. typhi genomes, based on a MUMmer whole genome alignment. For RNAz and the Dynalign/LIBSVM classifier, results are listed for three P value classification cutoffs. "Number of nucleotides" = number of nucleotides on the plus strand + number of nucleotides on the minus strand, not accounting for overlap of complementary strands.