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Table 1 Summary of the results of ProbeAlign and CMsearch on the RMARK3 dataset.

From: ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search

Rfam ID Name Identity # Tests # Predictions CMsearch ProbeAlign
      TP FP TP FP
RF00005 tRNA 44% 20 61 10 51 16 45
RF00007 U12 61% 7 8 7 1 6 2
RF00013 6S 43% 38 24 21 3 24 0
RF00017 SRP_euk_arch 46% 21 24 19 5 21 3
RF00020 U5 52% 22 23 19 4 22 1
RF00023 tmRNA 48% 59 59 58 1 57 2
RF00028 Intron_gpl 34% 20 5 4 1 5 0
RF00030 RNase_MRP 44% 28 36 16 20 22 14
RF00066 U7 62% 2 1 1 0 0 1
RF00080 yybP-ykoY 46% 13 13 13 0 10 3
RF00104 mir-10 58% 2 1 0 1 1 0
RF00114 S15 61% 8 11 8 3 7 4
RF00140 Alpha_RBS 65% 3 4 1 3 3 1
RF00165 Corona_pk3 68% 1 4 0 4 1 3
RF00177 SSU_rRNA_5 49% 13 17 12 5 13 4
RF00230 T-box 46% 48 50 46 4 47 3
RF00504 Glycine 50% 14 14 14 0 13 1
RF00515 PyrR 46% 29 38 25 13 28 10
RF00534 SgrS 48% 3 2 0 2 1 1
RF00548 U11 57% 8 11 7 4 5 6
RF00640 MIR167_1 53% 10 9 8 1 7 2
RF00645 MIR169_2 52% 21 21 21 0 20 1
RF00661 mir-31 57% 3 3 2 1 3 0
RF01052 Arthropod_7SK 65% 2 3 0 3 2 1
RF01066 6C 67% 1 2 1 1 0 2
RF01069 purD 56% 8 9 8 1 7 2
RF01296 snoU85 62% 2 6 1 5 2 4
  Overall   406 459 322 137 343 116
  1. Only the families with different results between the two programs are shown in the table.