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Table 1 Summary of reproducing results from the literature using RNArobo. Searches were extended by allowing for insertions in structurally conserved elements that are known to tolerate single base insertions. This extension led to improved sensitivity and yielded several new putatively functional ribozymes

From: RNA motif search with data-driven element ordering

Sequence Descriptor #hits Known targets found Note
In vitro selected library GTP apt. class I 9 yes  
(∼65 kBp scanned) GTP apt. class I w/ ins 10 yes [42] novel hit
Yarrowia lipolytica HHR I (4 bp) 1 Yli-1-3  
(∼41 MBp scanned) HHR I (4 bp) w/ ins 15 Yli-1-3 through Yli-1-11  
  HHR I (3 bp) 4 Yli-1-3 and Yli-1-13  
  HHR I (3 bp) w/ ins 54 Yli-1-3 through Yli-1-11, novel family
    and Yli-1-13 [16] (10 hits)
Bacillus cereus HHR II 1 Bce-1-1  
(∼11 MBp scanned) HHR II w/ ins 4 Bce-1-1 [16]  
Anopheles gambiae chr2L HDV (loose P4) 7 Agam-1-1  
(∼98 MBp bases scanned) HDV (loose P4) w/ ins 36 Agam-1-1 and Agam-1-2 [7]  
Strongylocentrotus purpuratus HDV (stem P4) 11 yes  
(∼2.1 GBp scanned) HDV (stem P4) w/ ins 11 yes  
  HDV (loose P4) + FF 15 yes  
  HDV (loose P4) w/ ins + FF 16 yes [7] novel hit
  1. FF: only hits passing the Fold-Filter are reported
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