CompaRNA - on-line benchmarks of RNA structure prediction methods
Home

Methods
Datasets
Rankings
RNA 2D Atlas

Help
FAQ

Contact us
RSS feeds
Twitter

RNA Secondary Structure Atlas - PDB - RNASampler(seed)



2KDQ_B [ FASTA input ] GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
[ reference std structure ] ((((((...((((......))))))))))
[ reference ext structure ] (((((([..(]((......)).)))))))
          (          )       
[ predicted structure ] ((((((...((((......))))))))))
2KE6_A [ FASTA input ] GGCUUGAUUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAAUUAAGCC
[ reference std structure ] (((((.(((((((((((((........))))))).))).))).)))))
[ reference ext structure ] (((((.(((((((((((((.(....).))))))).))).))).)))))
[ predicted structure ] ..(((((((((((((((((........))))))).))).)))))))..
2KUR_A [ FASTA input ] GGCUUGAUUGUAUUAUUAAAUUAAUUCUUAAUAACUACAAAUUAAGCC
[ reference std structure ] (((((((((((((((((((........))))))).))).)))))))))
[ reference ext structure ] (((((((((((((((((((((....))))))))).))).)))))))))
[ predicted structure ] ..(((((((((((((((((........))))))).))).)))))))..
2KUU_A [ FASTA input ] GGCUUGAUUGUAUGUGUAAAUUAAUUCUUACACACUACAAAUUAAGCC
[ reference std structure ] (((((.(((((((((((((........))))))).))).))).)))))
[ reference ext structure ] (((((.(((((((((((((((....))))))))).))).))).)))))
                    (     )                     
[ predicted structure ] ..(((((((((((((((((........))))))).))).)))))))..
2KUV_A [ FASTA input ] GGCUCGAUUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAAUCGAGCC
[ reference std structure ] (((((((((((((((((((........))))))).))).)))))))))
[ reference ext structure ] (((((((((((((((((((((....))))))))).))).)))))))))
                    (     )                     
[ predicted structure ] ..(((((((((((((((((........))))))).))).)))))))..
2KUW_A [ FASTA input ] GGGGUUGGUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAUCAGCUCC
[ reference std structure ] (((((((((((.(((((((........)))))))..)).)))))))))
[ reference ext structure ] (((((((((((((((((((.(....).))))))).))).)))))))))
                    (     )                     
[ predicted structure ] ..(((((((((((((((((........))))))).))).)))))))..
2L1F_A [ FASTA input ] GGCGGACCCGUGGUGGAACAGACGUGUUCGGAACACCCGGCCGCAACCCUGGGAGACGUCCCAGG
[ reference std structure ] .((((..(((.(((((((((....)))))....)))))))))))...(((((((....)))))))
[ reference ext structure ] .((((.()((.(((((((((....)))))....)))))).))))...(((((((....)))))))
       (                               )                         
[ predicted structure ] .((((..........(((((....)))))...........))))...(((((((....)))))))
2L1F_B [ FASTA input ] GGCGGACCCGUGGUGGAACAGACGUGUUCGGAACACCCGGCCGCAACCCUGGGAGACGUCCCAGGG
[ reference std structure ] .((((..(((.(((((((((....)))))....)))))))))))..((((((((....))))))))
[ reference ext structure ] .((((.()((.(((((((((....)))))....)))))).))))..((((((((....))))))))
       (                               )                          
[ predicted structure ] .((((..........(((((....)))))...........))))..((((((((....))))))))
2L94_A [ FASTA input ] GGGAAGAUCUGGCCUUCCCACAAGGGAAGGCCAGGGAAUCUUCCC
[ reference std structure ] ((((((((.((((((((((....))))))))))....))))))))
[ reference ext structure ] ((((((((((((((((((((..))))))))))))...))))))))
[ predicted structure ] .......((((((((((((....))))))))))))..........
2LC8_A [ FASTA input ] GGUCAGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGCA
[ reference std structure ] .(((.((((((((.[[[[[[[)))).))))..))).............]]]]]]].
[ reference ext structure ] .((((((((((((({{{{{.[)))).))))).))).............])}}}}}.
                   (                             )      
[ predicted structure ] ..(((((((.....)))).....)))...........(((........))).....
2MIY_A [ FASTA input ] GCUUGGUGCUUAGCUUCUUUCACCAAGCAUAUUACACGCGGAUAACCGCCAAAGGAGAA
[ reference std structure ] ((((((((.....[[[[[[.)))))))).........(((......)))..]]]]]]..
[ reference ext structure ] ((((((((.[{..<<<<...)))))))).........(((......)))..]}>>>>..
                 (                                  )      
                  (                                )       
[ predicted structure ] .(((((((............)))))))..........((((....))))..........
2N1Q_A [ FASTA input ] GGUGCCCGUCUGUUGUGUGACUCUGGUGAGAGCCAGAGGAGAUCUCUCGACGCAGGACUCGGCUUGCUGGAGACGGCAAGAGGCGAGGGGCGGCGACUGGUGAGUACGCCAAAAAUUUUGACUAGCGGAGGCUAGAAGGAGAGAGAUGGGUGCCC
[ reference std structure ] (((((((((((...((((..(((((((....)))))))...(((..(((.(((....((((.(((((((....)))))))...))))..))).)))..)))....)))).......(((..(((((....)))))..)))...))))))))))).
[ reference ext structure ] ((((((((((((((((((.(((((((((..)))))))))..((((((((((((((..(((((((((((((..)))))))))..))))))))))))))))))....)))).).....((((((((((....)))))))))).))))))))))))).
[ predicted structure ] ......(((((...................................................(((((((....)))))))...............................................................))))).......
3A3A_A [ FASTA input ] GCCCGGAUGAUCCUCAGUGGUCUGGGGUGCAGGCUUCAAACCUGUAGCUGUCUAGCGACAGAGUGGUUCAAUUCCACCUUUCGGGC
[ reference std structure ] (((((((.(..((((([..(.])))))((((((.......)))))).(((((....))))).((((..)....))))).)))))))
[ reference ext structure ] (((((((((..(((((({[{.))))))(((((((..)...))))))((((((....))))))(((((]}.)}.)))))))))))))
                   ()                                                                 
[ predicted structure ] (((((((....................((((((.......)))))).(((((....)))))..................)))))))
3IVN_B [ FASTA input ] GGCCAGUAUAACCUCAAUGAUAUGGUUUGAGGGUGUCUACCAGGAACCGUAAAAUCCUGACUACUGGUC
[ reference std structure ] (((((((({..((((((......[[.))))))(.....})(((((.]]......)))))..))))))))
[ reference ext structure ] (((((((([(.(((((((.{{..{{)))))))).(...].(((((.}}().}}.))))).)))))))))
                                    (                        )       
                                (      )                             
                                  (  )                               
[ predicted structure ] ((((((((...((((((.........))))))........(((((.........)))))..))))))))
3J3E_8 [ FASTA input ] AACUCUAAGCGGUGGAUCACUCGGCUCAUGGGUCGAUGAAGAACGCAGCAAACUGUGCGUCAUCGUGUGAACUGCAGGACACAUGAACAUCGACAUUUUGAACGCAUAUCGCAGUCCAUGCUG
[ reference std structure ] ........................................((((((.[[.....))).....(.((((.....]]...........))))..)...)))....((.....))...........
[ reference ext structure ] ..................................().<((((((((.{{(.).{))).[.}(].(((..(((.}}).)......).).))....).))))>).((.....))...........
                                                                  (                    )                                   
                                                                       (     )                                             
                                   (                                                                  )                    
                                                              (                             )                              
                                                                           ()                                              
                                                        ()                                                                 
                                                                   (                  )                                    
                                                          (                                  )                             
                                     (                                                                )                    
[ predicted structure ] .......((((.(((.....))).........((((((.....(((((....)))))........((((...))))...........)))))).....(((.......))).......)))).
3J3F_8 [ FASTA input ] CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCUU
[ reference std structure ] ..........................................((.((.[[.....))......(.(((......]].............)))..)...)).....((....))(((((.((.......)).))))).....................
[ reference ext structure ] ....................................(.{(((((.((.[[....[))).(.].(((((.(((..]].)........)).)))).))...)))}))((....))(((((((((.....))))))))).....................
                                                         ()                                                                                                  
                                           (                                                      )                                                          
                                                                       (      )                                                                              
                                            (            )                                                                                                   
[ predicted structure ] .........(((.(((.....))).........(((((((....(((((....)))))..............................)))))))..................(((((((((.....))))))))).....))).............
3JYX_4 [ FASTA input ] AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAUACGUAAUGUAGGUUGCAGAAUUCCGUGAAUCAUCGAUCUUUGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
[ reference std structure ] ..........................................(.(((........))).......(..........................)......)................(((((((....))))))).......................
[ reference ext structure ] .(..)..............................().<((((({(([.....[.).}..)..(.(((.((..]].......))......))).)...))))>)...(....)...((((((((..)))))))).......................
                                                                                                            (   )                                            
                                             (          )                                                                                                    
                                      (                                                                 )                                                    
                                                                    (                     )                                                                  
                                                                                                           (     )                                           
[ predicted structure ] ...(((...........................(((((((....((((......))))...............................)))))))..................(((((((((....)))))))))..........)))........
3O58_3 [ FASTA input ] AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAUACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
[ reference std structure ] .........................................((((([..(.....]))....((..((.........)............))...).).)))....(((...))).((((((((....))))))))......................
[ reference ext structure ] ....................................(.{((((([((.<<....<).]..)>((.(.(.........>.>..........))...))..))))}))(((...)))(((((((((....))))))))).....................
                                                         ()                                                                                                   
                                      (                                                                  )                                                    
                                             (          )                                                                                                     
                                                                  (                        )                                                                  
                                                              (                                  )                                                            
                                                (                             )                                                                               
[ predicted structure ] ........((((.....................(((((((....((((......))))...............................)))))))...................(((((((((....))))))))).....))))............
3RKF_A [ FASTA input ] GGCCAUAUAACUGCGUGGAUAUAGCACGCAGGUUUCUACCGGGCACUGUAAAUGUCCGACUAUGGUC
[ reference std structure ] ((((((([..(((((((.....{{)))))))(.....])((((((}}.....))))))..)))))))
[ reference ext structure ] (((((((((.(((((((.[[[.[[)))))))).....).((((((]]()]]]))))))..)))))))
                                   (                        )      
                                              (    )               
                               (      )                            
                                  (                          )     
                                              (   )                
                       (                           )               
[ predicted structure ] (((((((...(((((((.......)))))))........((((((.......))))))..)))))))
3SD1_A [ FASTA input ] GGAGAGUAGAUGAUUCGCGUUAAGUGUGUGUGAAUGGGAUGUCGUCACACAACGAAGCGAGAGCGCGGUGAAUCAUUGCAUCCGCUCCA
[ reference std structure ] ((((....((((((((((((......(((((((...[[[[....))))))).....((....))))).)))))))))..]]]].)))).
[ reference ext structure ] ((((((.({{{{{{{{{{{{..{{.{{{{{{{{.[.)((((].)}}}}}}}}.}}.(((..)))}}}.}}}}}}}}}.)))).))))).
                                                       (        )                        
                      (                                           )                      
                                 (         )                                             
                  (  )                                                                   
                                    (                                             )      
[ predicted structure ] ........((((((((((........(((((((...........)))))))................))))))))))............
3W3S_B [ FASTA input ] GGGAGAGGUUGGCCGGCUGGUGCCGCCCCGGGACUUCAAAUCCCGUGGGAGGUCCCGCAAGGGAGCUCCGGAGGGUUCGAUUCCCUCCCUCUCCCGCC
[ reference std structure ] (((.((((..((.((([..(.])))))((((((.......))))).)((((.((((....)))).)))).(((((..)....))))))))).)))...
[ reference ext structure ] (((.((((..((.(((([[()))))))((((((.......))))).)((((((((((..)))))))))).((((((]..)].))))))))).)))...
                   (                                                         )                    
                     (                                               )                            
[ predicted structure ] ((((((((....................(((((.......)))))..........................................))))))))...
3ZEX_C [ FASTA input ] AACGUGUCGCGAUGGAUGACUUGGCUUCCUAUUUCGUUGAAGAACGCAGCAAAGUGCGAUAAGUGGUAUCAAUUGCAGAAUCAUUUCAUUGCCCAAUCUUUGAACGCAAACGGCGCAUGGGAGAAGCUCUCUCGAGCCAUCCCCGUGCAUGCCACAUUUCUCAGUGUCG
[ reference std structure ] .........................................((((((.[[.....)))....(((((((...(.]].).........).)))).).).)))....((.....))(((((.(.(..((((....))))..).).))))).....................
[ reference ext structure ] ...................................[(..(.(((.((.{.(.){.)))(..}((((((..((..}..).......).)..))).))..))))].)(((..).))(((((((((.(((((....))))).))))))))).....................
                                                                                                                     (                           )                       
                                                         ()                                                                                                              
                                                 (                        )                                                                                              
                                      (                                                               )                                                                  
                                                                    (                  )                                                                                 
                                                                   (                     )                                                                               
                                       (                                                               )                                                                 
                                           (                                                      )                                                                      
                                                (                          )                                                                                             
                                                                        (    )                                                                                           
                                        (                                                            )                                                                   
                                             (              )                                                                                                            
                                                              (                                 )                                                                        
                                            (            )                                                                                                               
                                      (                                                                 )                                                                
[ predicted structure ] .((((................................(((....((((......))))....(((((....)))))............))).......................(((((((....................)))))))...............))))..
4A1C_2 [ FASTA input ] AGAAAAUUUUCAACGGUGGAUAUCUAGGUUCCCGUGACGAUGAAGAACGCAGCGAAAUGCGAUACGCAAUGCGAAUUGCAGAACCGCGAGUCAUCAGAUCUUUGAACGCAAGUGGUGGAGGUGUAAAAACCUUCAUGUUUGUUUCAGUGUGGAA
[ reference std structure ] ............................................((((((.[[.....))).....(.((((.....]]..........).)))..)...)))....((.....))(((((........)))))....................
[ reference ext structure ] .......................................(.<((((({((.[[....[).}..)](((((((.((..]]...)....).).)))).))..))))>))((.....))(((((........)))))....................
                                                            ()                                                                                            
                                         (                                                                )                                               
                                                                         (         )                                                                      
                                                (          )                                                                                              
[ predicted structure ] ...........((((.(((....)))............(((((....((((......))))....(((((....)))))...........)))))....................(((((((......)))))))....))))...........
4BY9_A [ FASTA input ] GCGAGCAAUGAUGAGUGAUGGGCGAACUGAGCUCGAAAGAGCAAUGAUGAGUGAUGGGCGAACUGAGCUCGC
[ reference std structure ] ((((((....................(...((((....))))......).................))))))
[ reference ext structure ] ((((((...((((.............(((((((((..)))))...)))).............))))))))))
                          (                      )                      
[ predicted structure ] .............(((..............((((....))))...................)))........
4C4Q_N [ FASTA input ] GACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCACUAGCCCACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUGGCGGGGGUCGCUAGGGUGAAAUCACAUUAUGUGAUGGGGGUACGACCUGAUAGGGUGCUGCAGAGGCCCACUAGCAGGCUAGUAUAAAAAUCUCUGC
[ reference std structure ] .(((((((.((((((((.((((((.(((((((((..((((((....))))))..(((((..((((((((.(((.((....)).))).))))...))))....)))))(((....))).)))).)))))..((((((((((...))))))))))....(((((...))))).)))))).)).(((....))).((..[[[[.))))))))...))))))).........]]]].
[ reference ext structure ] .(((((((.((((((((.((((((.(((((((((..((((((....))))))..(((((.(((((((((.(((((((..))))))).))))...)))))...)))))(((....))).))))).))))..((((((((((...))))))))))....(((((...))))).)))))).))(((((..)))))((..[[[[[))))))))...)))))))........]]]]].
                             (                                                                                             )                                                                                                             
                          (                                                                                                      )                                                                                                       
    (                                                                                                                                                                                                                            )       
                                                                                                              (   )                                                                                                                      
[ predicted structure ] .(((((((.((((((...((((((.(((((((((..((((((....))))))..(((((.(((((((((.(((..........))).))))...)))))...)))))(((....))).)))).)))))..((((((((((...))))))))))...((((((...))))))))))))...((((....))))...........))))))...)))))))..............
4JF2_A [ FASTA input ] GAACCGCGAAAGCGGUUCCACGACGAUACUUAUUUCCUUUGAUCGUCGUUAUUACUGGCUUCGGCCACAAAGGAGA
[ reference std structure ] (((((((....))))))).((((((((.......[[[[[..))))))))......((((....))))..]]]]]..
[ reference ext structure ] ((((((((..)))))))).(((((((((.((...<<<...)))))))))....(.(((((..)))))).))>>>..
                                                      (            )        
                                      (                              )      
                                     (                                )     
[ predicted structure ] .....................((((((..............))))))........((((....)))).........
4P5J_A [ FASTA input ] AGCUCGCCAGUUAGCGAGGUCUGUCUCGACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCGGAACC
[ reference std structure ] .((((((..[...)))))(((((((.......)))))))...{{{{..]....}}}}(((...{{{{{{))).).}}}}}}..
[ reference ext structure ] .(((((([[()..)))))(((((((.......)))))))...{{{{{]..}].}}}}(((..{{{{{{{))).).}}}}}}.}
                                                                       ()          
                                                                      (   )        
         (                                      )                                  
[ predicted structure ] ..(((((......)))))(((((((.......)))))))...((((.......))))......((((((......))))))..
4P8Z_A [ FASTA input ] GGUUGGGUUGGGAAGUAUCAUGGCUAAUCACCAUGAUGCAAUCGGGUUGAACACUUAAUUGGGUUAAAACGGUGGGGGACGAUCCCGUAACAUCCGUCCUAACGGCGACAGACUGCACGGCCCUGCCUCUUAGGUGUGUCCAAUGAACAGUCGUUCCGAAAGGAAGCAUCCGGUAUCCCAAGACAAUC
[ reference std structure ] (((((..(((((..(((((((((...[[[.)))))))))..{{{{.{{{.{{{{......{{{{{...{{{{..{{{...]]]}}}.......}}}}((....)).....<<<<<...}}}}}.(((.....)))}}}}.}}}....>>>>>.((((....))))....}}}}...)))))..)))))
[ reference ext structure ] ((((((((((((..(((((((((...[.[.))))))))).{<<<<<<<<<<<<<(..<)<<<<<<.<.<<<<a.aaa...]].AAA...>.A..>>>aa...>AA....aaaaaa.()>>>>>>a.(.....)>A>>>>>>>>>.}.AAAAA.(((((..)))))..A.>>>>...))))))))))))
                           (                                                     )                                                                                                          
                                                                                                   (  )                                                                                     
                                                                                                                                                (                        )                  
                                                                                                                                                 (                           )              
                          (                                                       )                                                                                                         
                                                                       (                     )                                                                                              
                                                                                                                                                  (                       )                 
                                                                                                                             (       )                                                      
[ predicted structure ] (((((..((((((.(((((((((.......)))))))))....(((((....((((....))))......................................................)))))..............................((((....))))..........))))))..)))))
4W24_8 [ FASTA input ] CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU
[ reference std structure ] ............................................(((.[[....[)))...]...{{{......]].............}}}.............((....))(.....((.......)).....)....................
[ reference ext structure ] ....................................(..(.(.(.((.[[....[))).{.]...{{{{{{{..]]..}.......}}}}}}...}....))..)((....))(((...((((.)..)))...)))....................
                                                         ()                                                                                                 
                                           (                                                      )                                                         
                                             (              )                                                                                               
                                            (            )                                                                                                  
[ predicted structure ] .(((.........(((.....))).........(((((((....(((((....)))))..............................)))))))..................(((((((((.....)))))))))..............)))...
5DI4_A [ FASTA input ] GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACGAAACGCCCA
[ reference std structure ] ...............(....).(((((......)))))..........
[ reference ext structure ] .........(.....(....)[[[[[[[)..].]]]]]].........
[ predicted structure ] ................................................


  • N/A - RNA 2D structure in Vienna format could not have been generated (most likely due to difficult to represent pseudoknot structure). Check secondary structure file for details.
  • std - standard base pair definition
  • ext - extended base pair definition