Skip to main content

Table 7 Comparison of three ncRNA detection programs on a whole genome screen using WuBLASTn genomic windows.

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) 147 (94.23) 148 (94.87) 141 (90.38) 140 (89.74) 128 (82.05) 124 (79.49) 121 (77.56)
S. typhi (110 ncRNAs known) 109 (99.09) 108 (98.18) 107 (97.27) 106 (96.36) 103 (93.64) 95 (86.36) 100 (90.91)
Number of contiguous, non-overlapping hits that are not known ncRNAs (i.e. novel ncRNA candidates)
E. coli 2,569 1,898 1,828 1,568 1,211 1,257 1,403
S. typhi 3,936 2,503 2,440 1,986 1,520 1,520 1,611
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) 324,033 275,704 235,227 221,802 167,157 174,682 206,840
S. typhi (each strand = 4,809,037 nt) 514,650 387,099 352,039 296,608 235,018 220,485 248,724
Total number of nucleotides classified as ncRNA (i.e. nucleotides in both known and unknown ncRNAs)
E. coli (each strand = 4,639,675 nt) 385,611 332,000 292,940 270,267 220,352 209,807 242,534
S. typhi (each strand = 4,809,037 nt) 570,994 436,137 405,022 338,254 283,999 250,610 283,508
  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 genomic scanning windows prepared using WuBLASTn. 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.