| --- |
| library_name: multimolecule |
| license: agpl-3.0 |
| pipeline: rna-secondary-structure |
| pipeline_tag: other |
| tags: |
| - Biology |
| - RNA |
| - rna-secondary-structure |
| - rna |
| widget: |
| - example_title: microRNA 21 |
| output: |
| text: '......................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: UAGCUUAUCAGACUGAUGUUGA |
| - example_title: microRNA 146a |
| output: |
| text: '......................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: UGAGAACUGAAUUCCAUGGGUU |
| - example_title: microRNA 155 |
| output: |
| text: '........................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: UUAAUGCUAAUCGUGAUAGGGGUU |
| - example_title: RNA component of mitochondrial RNA processing endoribonuclease |
| output: |
| text: '..............(((((.....)))))............(.[..[{)({[{{<A((BC[[[({[<D<E[{AB<{CBCCCDBD<FACDEEFFGGDFGHIHIEFJFGIJJJKKLGHIJJMKJNOKLMLNJ.JMMNNO.......)KPONO]}})>]>)a]}>]>abcb.d.cc..defeghif.jjgfjfjghkklimmnnologeoipmknjjfkkdnlj..mcno])b]]}}]>a}cb.c.d}de.h........jjigf...............' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: GGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUAAAAAAAAA |
| - example_title: 7SK small nuclear RNA |
| output: |
| text: '.........(((((((..[[[[[[.(....)..........))))))).......({<<ABCDC(ABBA{C{CA<EF.EGGG...H][.HI[GG[FJJ[[KLMNO.FGHGGFHH.KKFKJGHJKKILMFMKMGHNMIJLNOIMIKMOLNMMPQRMONOOPQPPRRSQ..SRSSRTSS)})>}}({U>aa{><aabcbbcc]cde]f]gh]f]gieiffijfhgkhghlghmfnggioghgijkpgmkqjlrlpsrmjompqsn)mm}>osmrt}kumsnkkmsokrspqrnoklmjnoh...............]]]]].............' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: GGAUGUGAGGGCGAUCUGGCUGCGACAUCUGUCACCCCAUUGAUCGCCAGGGUUGAUUCGGCUGAUCUGGCUGGCUAGGCGGGUGUCCCCUUCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGCGCUCGGUCGAAGAGGACGACCAUCCCCGAUAGAGGAGGACCGGUCUUCGGUCAAGGGUAUACGAGUAGCUGCGCUCCCCUGCUAGAACCUCCAAACAAGCUCUCAAGGUCCAUUUGUAGGAGAACGUAGGGUAGUCAAGCUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGCAUGUGGCAGUCUGCCUUUCUUUU |
| - example_title: telomerase RNA component |
| output: |
| text: .(......................[{<AB{<A<A................)..(([([{({([{(...([{<[[AACCDAC<B[BBC(AEDEFFEGHHIFDDEDDEFGGEGHDIFE(JF{AKABB[LLL[DMNBO{EJMADFGMC<DNFGM)GEFHCH]IGFPDE])})]]]}NO>P])})]}HI>aGaGHbbJca>))]}cadKaKKdLIJLKLaeeMbMMNOPMNMQQMRNQROORPb)b]a]}bcd}d)>a(([([(STfSTTSSeTUUTUVVWTTf}>>{{{g<WXgfhdgddaiahfiebjjkekkeldkeddlflgmnhmopmonmnompmqi)h)gqq])rcgfceffgedgfhfiggjejkh.h.i.lllmnAopAAA.mA....msn.s..mttnoptuv)}.>t}uwv]ustw.}.ctsxtr.a.raaa...a........ |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC |
| - example_title: vault RNA 2-1 |
| output: |
| text: .(((((((..(.(((.(..((((....(((........((((.........))))..................)))..))))..).))).)))))))).......... |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: CGGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUUAUGCAA |
| - example_title: brain cytoplasmic RNA 1 |
| output: |
| text: '....(.........([.{{([([[({([([[...((.....)).....(........<....)....................................................)]))])]]]}).])]}}....)............................................>..................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCUCUCAGGGAGGCUAAGAGGCGGGAGGAUAGCUUGAGCCCAGGAGUUCGAGACCUGCCUGGGCAAUAUAGCGAGACCCCGUUCUCCAGAAAAAGGAAAAAAAAAAACAAAAGACAAAAAAAAAAUAAGCGUAACUUCCCUCAAAGCAACAACCCCCCCCCCCCUUU |
| - example_title: HIV-1 TAR-WT |
| output: |
| text: (((.(((((((((((.(((((....(..........).))))))))))))))))))) |
| pipeline_tag: rna-secondary-structure |
| sequence_type: ncRNA |
| task: rna-secondary-structure |
| text: GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACC |
| - example_title: prion protein (Kanno blood group) |
| output: |
| text: '..........(.((...........(((((........)))))..........)).).........' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: mRNA |
| task: rna-secondary-structure |
| text: AUGGCGAACCUUGGCUGCUGGAUGCUGGUUCUCUUUGUGGCCACAUGGAGUGACCUGGGCCUCUGC |
| - example_title: interleukin 10 |
| output: |
| text: '......................................................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: mRNA |
| task: rna-secondary-structure |
| text: AUGCACAGCUCAGCACUGCUCUGUUGCCUGGUCCUCCUGACUGGGGUGAGGGCC |
| - example_title: Zaire ebolavirus |
| output: |
| text: '........((((((..........(.(...............((((..........))))[[{..<A<[B{{<B{{)B)(C((<<D(ABBCACBCD{{<DAACADBCBCDEBEEFFCDFGHEIFJHHH...II...........................................])}})}>a}>bb>c)}db}>]a]}caefdefaaebbcccbedddgc>c>af)bcbhfdhihibhij(([{(.[...(..[[..[.(..................))]]])])]}).......))))))..' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: mRNA |
| task: rna-secondary-structure |
| text: AAUGUUCAAACACUUUGUGAAGCUCUGUUAGCUGAUGGUCUUGCUAAAGCAUUUCCUAGCAAUAUGAUGGUAGUCACAGAGCGUGAGCAAAAAGAAAGCUUAUUGCAUCAAGCAUCAUGGCACCACACAAGUGAUGAUUUUGGUGAGCAUGCCACAGUUAGAGGGAGUAGCUUUGUAACUGAUUUAGAGAAAUACAAUCUUGCAUUUAGAUAUGAGUUUACAGCACCUUUUAUAGAAUAUUGUAACCGUUGCUAUGGUGUUAAGAAUGUUUUUAAUUGGAUGCAUUAUACAAUCCCACAGUGUUAU |
| - example_title: SARS coronavirus |
| output: |
| text: '.......................................(....[[{..<<A..B.CDCDEEFFF....GC.D..HHIJIKKLJJKKLMJNNOKMPONPQQIQORPNQSRTSJRRTUSSUTVWWWWXUYUV..........(((......W.)))..V.......WXXYXYZX.ZX.YZ..Y)(].(((.U.VT}{][.[.......[{.[>.aAbcdcdce>defffghi{{i<iBjjjkjjh<Ak<lmm{{{<{{A<AABBCDDDCED.F.....nnnoopnqropGFHFHHIIHFGsJsHrHFIIGJHG)ttuv)uuv]}k}klkwvxxyyx>abxyzcdcdedbyda}}>}}a>}>w>a................f]g}]f..ga.ghfhffigijhhhijhhi]z.b)z}.qx...r)p.qq..s...rs......tu..u..vwtxyww(w((((.(.(((((....))))).).)))).)........' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: mRNA |
| task: rna-secondary-structure |
| text: AUGUUUAUUUUCUUAUUAUUUCUUACUCUCACUAGUGGUAGUGACCUUGACCGGUGCACCACUUUUGAUGAUGUUCAAGCUCCUAAUUACACUCAACAUACUUCAUCUAUGAGGGGGGUUUACUAUCCUGAUGAAAUUUUUAGAUCAGACACUCUUUAUUUAACUCAGGAUUUAUUUCUUCCAUUUUAUUCUAAUGUUACAGGGUUUCAUACUAUUAAUCAUACGUUUGACAACCCUGUCAUACCUUUUAAGGAUGGUAUUUAUUUUGCUGCCACAGAGAAAUCAAAUGUUGUCCGUGGUUGGGUUUUUGGUUCUACCAUGAACAACAAGUCACAGUCGGUGAUUAUUAUUAACAAUUCUACUAAUGUUGUUAUACGAGCAUGUAACUUUGAAUUGUGUGACAACCCUUUCUUUGCUGUUUCUAAACCCAUGGGUACACAGACACAUACUAUGAUAUUCGAUAAUGCAUUUAAAUGCACUUUCGAGUACAUAUCU |
| - example_title: insulin |
| output: |
| text: '....................................................................(.......[.{[..[{<{[[{A)((<[B{ABBCABC<(D[A<E{DDCADCBFFGCGDDFDEEEFGEHGGHHI(I[G{HJ)K]H}IJLLMM..M.KNLLLLMNONNO))]]}}]}>a>)b]]a]>ab}}>ccadcbedbdee(f)g()ehgh(]a)ijh}ikgljkmnlllnigobhcnodllmcdddefnfmmfhgg....................................................................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: mRNA |
| task: rna-secondary-structure |
| text: AUGGCCCUGUGGAUGCGCCUCCUGCCCCUGCUGGCGCUGCUGGCCCUCUGGGGACCUGACCCAGCCGCAGCCUUUGUGAACCAACACCUGUGCGGCUCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCCCUUGGCCCUGGAGGGGUCCCUGCAGAAGCGUGGCAUUGUGGAACAAUGCUGUACCAGCAUCUGCUCCCUCUACCAGCUGGAGAACUACUGCAACUAG |
| - example_title: cyclin dependent kinase inhibitor 2A |
| output: |
| text: ..(...................((.....(((...)))......)).......[..[[.[[[([{(([{<AB[BBCC[<C(D<BAEC(C<D[[EE{FC(FFAB)ADGACA)C]]FBCEFBDGCEEDFDEDGHEFFDGEFGEFHHHIGJKGH))]})I]]}{KG)L]L(LJKMMJJLIMMLN(LKJKMKN)NKOLMNOIOPLMO>PPQQRaQRPSTUOUQTPVPURPTaQSUTPQQabaWcRRddSbTdTee}Tffd)ecTUUVVWWb..)([..{.)]}(>(>[[)>gec]]af]g}hdg]ga]ebii]j]e]cck(fcdlijlmkhmkbjcjnobciepq(pqfqprrstu)kvkwtjvdtbkwoplpml)pq)olqdrsnultrqstcecmqtnpufprotftnmohhefffgggelhkm......lu.mguu.v..w............................... |
| pipeline_tag: rna-secondary-structure |
| sequence_type: mRNA |
| task: rna-secondary-structure |
| text: AUGGAGCCGGCGGCGGGGAGCAGCAUGGAGCCUUCGGCUGACUGGCUGGCCACGGCCGCGGCCCGGGGUCGGGUAGAGGAGGUGCGGGCGCUGCUGGAGGCGGGGGCGCUGCCCAACGCACCGAAUAGUUACGGUCGGAGGCCGAUCCAGGUCAUGAUGAUGGGCAGCGCCCGAGUGGCGGAGCUGCUGCUGCUCCACGGCGCGGAGCCCAACUGCGCCGACCCCGCCACUCUCACCCGACCCGUGCACGACGCUGCCCGGGAGGGCUUCCUGGACACGCUGGUGGUGCUGCACCGGGCCGGGGCGCGGCUGGACGUGCGCGAUGCCUGGGGCCGUCUGCCCGUGGACCUGGCUGAGGAGCUGGGCCAUCGCGAUGUCGCACGGUACCUGCGCGCGGCUGCGGGGGGCACCAGAGGCAGUAACCAUGCCCGCAUAGAUGCCGCGGAAGGUCCCUCAGACAUCCCCGAUUGA |
| - example_title: human papillomavirus type 16 E6 |
| output: |
| text: '...........................................(([..........................(({(<(..[{<{{{AAB(<(<BBC[DC({D<EE{FGG<HHIAFBFCAEFDGDDCEEEFEEFGDGDHHIEEIFH.G.HG...I..JKGKJHLIMMNMN)...)..)JKJKL]MMLJMLKNN)OPP((O}OPN}>PQ>QQQRSTaaAUVV]WWWXWXX}}..}b>>}>..{<{{{<YZc{YZZ<defedgggG...G.h..i.jkjkljll)mnmnopknqm)orqqstaqpuvvQRhQSTiabjbjakABBlkc)dmmnm)nede))fe])}}}>wwx}wc>g}xdxywezzgghhedh>figyze.i....cf.ef}.gfo>ppqfgqhihedrabbgstb................................................................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: mRNA |
| task: rna-secondary-structure |
| text: AUGCACCAAAAGAGAACUGCAAUGUUUCAGGACCCACAGGAGCGACCCAGAAAGUUACCACAGUUAUGCACAGAGCUGCAAACAACUAUACAUGAUAUAAUAUUAGAAUGUGUGUACUGCAAGCAACAGUUACUGCGACGUGAGGUAUAUGACUUUGCUUUUCGGGAUUUAUGCAUAGUAUAUAGAGAUGGGAAUCCAUAUGCUGUAUGUGAUAAAUGUUUAAAGUUUUAUUCUAAAAUUAGUGAGUAUAGACAUUAUUGUUAUAGUUUGUAUGGAACAACAUUAGAACAGCAAUACAACAAACCGUUGUGUGAUUUGUUAAUUAGGUGUAUUAACUGUCAAAAGCCACUGUGUCCUGAAGAAAAGCAAAGACAUCUGGACAAAAAGCAAAGAUUCCAUAAUAUAAGGGGUCGGUGGACCGGUCGAUGUAUGUCUUGUUGCAGAUCAUCAAGAACACGUAGAGAAACCCAGCUGUAA |
| - example_title: NRAS proto-oncogene |
| output: |
| text: ((((((((((.((((.......................)))).))))))..))))............................................................................ |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 5' UTR |
| task: rna-secondary-structure |
| text: GGGGCCGGAAGUGCCGCUCCUUGGUGGGGGCUGUUCAUGGCGGUUCCGGGGUCUCCAACAUUUUUCCCGGCUGUGGUCCUAAAUCUGUCCAAAGCAGAGGCAGUGGAGCUUGAGGUUCUUGCUGGUGUGAA |
| - example_title: amyloid beta precursor protein |
| output: |
| text: '......................(...................................(((.................................................................)))..)..................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 5' UTR |
| task: rna-secondary-structure |
| text: GUCAGUUUCCUCGGCAGCGGUAGGCGAGAGCACGCGGAGGAGCGUGCGCGGGGGCCCCGGGAGACGGCGGCGGUGGCGGCGCGGGCAGAGCAAGGACGCGGCGGAUCCCACUCGCACAGCAGCGCACUCGGUGCCCCGCGCAGGGUCGCG |
| - example_title: RUNX family transcription factor 1 |
| output: |
| text: '.......................................(((.....)))................................................................................................................................................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 5' UTR |
| task: rna-secondary-structure |
| text: ACUUCUUUGGGCCUCAUAAACAACCACAGAACCACAAGUUGGGUAGCCUGGCAGUGUCAGAAGUCUGAACCCAGCAUAGUGGUCAGCAGGCAGGACGAAUCACACUGAAUGCAAACCACAGGGUUUCGCAGCGUGGUAAAAGAAAUCAUUGAGUCCCCCGCCUUCAGAAGAGGGUGCAUUUUCAGGAGGAAGCG |
| - example_title: fragile X messenger ribonucleoprotein 1 |
| output: |
| text: '....(((..........([[((..((((........))))))..............................{{<<{ABC{D<A<BBABCCBDBCDDECEFGFGHIIJHBJ(KJKJ())(K[)](())LMNKLE)(FMNNNFG.(]][)]()(())}>(>)ababccb}dbe)ffg((ee}fccgf}>hb>ahijbkjkllmnnnmdnjkjdikgb........c.d))...................)))..........' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 5' UTR |
| task: rna-secondary-structure |
| text: CUCAGUCAGGCGCUCAGCUCCGUUUCGGUUUCACUUCCGGUGGAGGGCCGCCUCUGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGCGGCGGUGACGGAGGCGCCGCUGCCAGGGGGCGUGCGGCAGCGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCUGGGCCUCGAGCGCCCGCAGCCCACCUCUCGGGGGCGGGCUCCCGGCGCUAGCAGGGCUGAAGAGAAG |
| - example_title: MYC proto-oncogene |
| output: |
| text: ..(.....[.[..{[[{<{{A[B[)..(C([.[B{{C{<AB.))]]}]}>ab]}]}]}}>a]}b]cbc((.[...........{{<<{A{B<A{ABBB<ACBB([DDCB[D{(...DEFGEH..EI.DD..C((...))...DE(FGCD[F(H[GICD[DEF{GHI<J{E<FEE<G<GAEEE<FAGBHIKCLLMCELMEMKHMHNMFNHNODLOPI))]}]>a>abJ}>]QO>>))Nc]]}))(c]((}>ab}}bbcc}d>dedefeefeghhdhheeeifegicfgdjaghijabklkcblbmn}e>>fmlal))gmfgnbcdhoimn)moddedddopeenfghqi............... |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 5' UTR |
| task: rna-secondary-structure |
| text: AACUCGCUGUAGUAAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGCCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUGAUCCCCCAGCCAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGCACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUAUUCUGCCCAUUUGGGGACACUUCCCCGCCGCUGCCAGGACCCGCUUCUCUGAAAGGCUCUCCUUGCAGCUGCUUAGACG |
| - example_title: activating transcription factor 4 |
| output: |
| text: '......................................................([([[.{<<<<.<ABABCBBDDEFEEEG(([AGFHECBBACBCDGAACBED.()......................................[).)..]]..)]..}.>a)aabbccaddbeb]ca]bbcbcdeedeee>affgg>>>hb.......g......................................................................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 5' UTR |
| task: rna-secondary-structure |
| text: CAUUUCUACUUUGCCCGCCCACAGAUGUAGUUUUCUCUGCGCGUGUGCGUUUUCCCUCCUCCCCGCCCUCAGGGUCCACGGCCACCAUGGCGUAUUAGGGGCAGCAGUGCCUGCGGCAGCAUUGGCCUUUGCAGCGGCGGCAGCAGCACCAGGCUCUGCAGCGGCAACCCCCAGCGGCUUAAGCCAUGGCGCUUCUCACGGCAUUCAGCAGCAGCGUUGCUGUAACCGACAAAGACACCUUCGAAUUAAGCACAUUCCUCGAUUCCAGCAAAGCACCGCAAC |
| - example_title: Human GPI protein p137 |
| output: |
| text: '........................................(((.(((((..........))))))))..............([{<A<ABCBDEFGG.(.EH)H.I.........JKJLMKM(NNOP.[...................................................................)...]...)]}>a>.abbcdeefgghhijjkklmmnonp..................................................................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 3' UTR |
| task: rna-secondary-structure |
| text: UUUUUAAAAGGAAAAGAUACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUUUGAAAGGCACCAGUAUGUGUUUUAGAUUGAUUUAAAUGUUUCAUUUAAAUCACGGACAGUAGUUUCAGUUCUGAUGGUAUAAGCAAAACAAAUAAAACGUUUAUAAAAGUUGUAUCUUGAAACACUGGUGUUCAACAGCUAGCAGCUUAUGUGAUUCACCCCAUGCCACGUUAGUGUCACAAAUUUUAUGGUUUAUCUCCAGCAACAUUUCUCUAGUACUUGCACUUAUUAUCUGAAUUC |
| - example_title: nucleophosmin 1 |
| output: |
| text: '......................................................(((((((.....))))))).....................((..[..........................(({([<[{[.{<A{<A{(<<[<B(C[AA{D{...........EDEFFFG.HIHFB(B<C[<JJ{GAKL<BHAKBF{AMCNBCMJAICDN)]}BLJD}GE>)]}aa>)]bb)a)c>]}}>dc>>})baa]]be}}>>)a])b}d>abccabcdefdfggehfijffghhijjkk..jll.mmnn...........................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 3' UTR |
| task: rna-secondary-structure |
| text: GAAAAUAGUUUAAACAAUUUGUUAAAAAAUUUUCCGUCUUAUUUCAUUUCUGUAACAGUUGAUAUCUGGCUGUCCUUUUUAUAAUGCAGAGUGAGAACUUUCCCUACCGUGUUUGAUAAAUGUUGUCCAGGUUCUAUUGCCAAGAAUGUGUUGUCCAAAAUGCCUGUUUAGUUUUUAAAGAUGGAACUCCACCCUUUGCUUGGUUUUAAGUAUGUAUGGAAUGUUAUGAUAGGACAUAGUAGUAGCGGUGGUCAGACAUGGAAAUGGUGGGGAGACAAAAAUAUACAUGUGAAAUAAAACUCAGUAUUUUAAUAAAGUAGCACGGUUUCUAUUGA |
| - example_title: superoxide dismutase 1 |
| output: |
| text: '.................(..((((.........)))).)(([[{{[[<AA......................(...[{[([[({{<A((<AABBC(ADECDEFEFGFFHGGHHHIJ(..J)H.K............KKKLLMMNNNO....NO...............................................)))))]}})]]]>a}abcdeac>faeggfhbhhfdiejghfjhkklmklno.mnnno........))].]...]]}}>kaa........................................................................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 3' UTR |
| task: rna-secondary-structure |
| text: ACAUUCCCUUGGAUGUAGUCUGAGGCCCCUUAACUCAUCUGUUAUCCUGCUAGCUGUAGAAAUGUAUCCUGAUAAACAUUAAACACUGUAAUCUUAAAAGUGUAAUUGUGUGACUUUUUCAGAGUUGCUUUAAAGUACCUGUAGUGAGAAACUGAUUUAUGAUCACUUGGAAGAUUUGUAUAGUUUUAUAAAACUCAGUUAAAAUGUCUGUUUCAAUGACCUGUAUUUUGCCAGACUUAAAUCACAGAUGGGUAUUAAACUUGUCAGAAUUUCUUUGUCAUUCAAGCCUGUGAAUAAAAACCCUGUAUGGCACUUAUUAUGAGGCUAUUAAAAGAAUCCAAAUUCAAACUAAA |
| - example_title: hemoglobin subunit alpha 2 |
| output: |
| text: ..(.....................................).................................................................... |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 3' UTR |
| task: rna-secondary-structure |
| text: CUGGAGCCUCGGUAGCCGUUCCUCCUGCCCGCUGGGCCUCCCAACGGGCCCUCCUCCCCUCCUUGCACCGGCCCUUCCUGGUCUUUGAAUAAAGUCUGAGUGGGCAGCA |
| - example_title: BRAF proto-oncogene |
| output: |
| text: '......................................................([((({{<...)))[)(([({A[(.....B..([.({<A<B(A[C{{{AC<ADDBEFFDG)]}HH>IaJb}KKK)I)LMNODE)]}PP}>aa>abcc))])]]}((CCN(CQ(PRNNNOSTOLUCTO(RTU(VCUCLM(OBSMUBVUCCLTQTPWXPSNXNOSOWVYRPXdQQQUeWRWSTQRVZSS.d...dd.effghDDDDEFG][FGG[FE[[.}.}>i.h.ijk..a)bbcl)cbcc))cl)mnoclpm))knlmncqokoqqnporssqcnnopn]rsoo]pqpp]trqrrssststuvtuvuuvdwwuwttwxvuexxyzefdd]fgfdgg...........................' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 3' UTR |
| task: rna-secondary-structure |
| text: AACAAAUGAGUGAGAGAGUUCAGGAGAGUAGCAACAAAAGGAAAAUAAAUGAACAUAUGUUUGCUUAUAUGUUAAAUUGAAUAAAAUACUCUCUUUUUUUUUAAGGUGAACCAAAGAACACUUGUGUGGUUAAAGACUAGAUAUAAUUUUUCCCCAAACUAAAAUUUAUACUUAACAUUGGAUUUUUAACAUCCAAGGGUUAAAAUACAUAGACAUUGCUAAAAAUUGGCAGAGCCUCUUCUAGAGGCUUUACUUUCUGUUCCGGGUUUGUAUCAUUCACUUGGUUAUUUUAAGUAGUAAACUUCAGUUUCUCAUGCAACUUUUGUUGCCAGCUAUCACAUGUCCACUAGGGACUCCAGAAGAAGACCCUACCUAUGCCUGUGUUUGCAGGUGAGAAGUUGGCAGUCGGUUAGCCUGGG |
| - example_title: H3 clustered histone 1 |
| output: |
| text: '.....(((((..((((((.............[[......))))))]])))))......' |
| pipeline_tag: rna-secondary-structure |
| sequence_type: 3' UTR |
| task: rna-secondary-structure |
| text: UUACUGUGGUCUCUCUGACGGUCCAAGCAAAGGCUCUUUUCAGAGCCACCACCUUUUC |
| --- |
| |
| # UFold |
|
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| Pre-trained model for RNA secondary structure prediction using an image-like sequence representation and a U-Net. |
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| ## Disclaimer |
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| This is an UNOFFICIAL implementation of [UFold: fast and accurate RNA secondary structure prediction with deep learning](https://doi.org/10.1093/nar/gkab1074) by Laiyi Fu, Yingxin Cao, et al. |
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| The OFFICIAL repository of UFold is at [uci-cbcl/UFold](https://github.com/uci-cbcl/UFold). |
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| > [!TIP] |
| > The MultiMolecule implementation is a direct PyTorch port of the original U-Net architecture and feature construction. |
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| **The team releasing UFold did not write this model card for this model so this model card has been written by the MultiMolecule team.** |
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| ## Model Details |
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| UFold predicts RNA base-pair contact maps from single RNA sequences. It represents a sequence as a 17-channel image: 16 channels are outer products of one-hot nucleotide indicators and one channel is a hand-crafted canonical/wobble pairing score. A U-Net predicts a symmetric contact score matrix, and the original constrained post-processing routine can be enabled to enforce base-pairing constraints. |
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| ### Model Specification |
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| | Num Parameters (M) | FLOPs (G) | MACs (G) | |
| | ------------------ | --------- | -------- | |
| | 8.64 | 188.29 | 93.81 | |
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| FLOPs and MACs are computed with `multimolecule.utils` for one 600 nt sequence. |
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| ### Links |
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| - **Code**: [multimolecule.ufold](https://github.com/DLS5-Omics/multimolecule/tree/master/multimolecule/models/ufold) |
| - **Weights**: [multimolecule/ufold](https://huggingface.co/multimolecule/ufold) |
| - **Paper**: [UFold: fast and accurate RNA secondary structure prediction with deep learning](https://doi.org/10.1093/nar/gkab1074) |
| - **Developed by**: Laiyi Fu, Yingxin Cao, Jie Wu, Qinke Peng, Qing Nie, Xiaohui Xie |
| - **Original Repository**: [uci-cbcl/UFold](https://github.com/uci-cbcl/UFold) |
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| ## Usage |
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| The model file depends on the [`multimolecule`](https://multimolecule.danling.org) library. You can install it using pip: |
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| ```bash |
| pip install multimolecule |
| ``` |
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| ### RNA Secondary Structure Pipeline |
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| ```python |
| import multimolecule |
| from transformers import pipeline |
| |
| predictor = pipeline("rna-secondary-structure", model="multimolecule/ufold") |
| output = predictor("GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCUCA") |
| ``` |
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| ### PyTorch Inference |
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| ```python |
| from multimolecule import RnaTokenizer, UfoldModel |
| |
| tokenizer = RnaTokenizer.from_pretrained("multimolecule/ufold") |
| model = UfoldModel.from_pretrained("multimolecule/ufold") |
| |
| sequence = "GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCUCA" |
| inputs = tokenizer(sequence, return_tensors="pt") |
| output = model(**inputs) |
| |
| contact_map = output.contact_map |
| ``` |
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| To run the original constrained post-processing loop: |
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| ```python |
| output = model(**inputs, use_postprocessing=True) |
| contact_map = output.postprocessed_contact_map |
| ``` |
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| ## Training Details |
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| UFold was trained for RNA secondary structure prediction from annotated contact maps and base-pairing rules. |
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| ### Training Data |
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| - RNAStrAlign: 30,451 unique RNAs from eight RNA families; the paper reports a random split with 24,895 training RNAs and 2,854 test RNAs after redundancy filtering. |
| - bpRNA-1m: 102,318 RNAs from 2,588 families; CD-HIT was used to remove redundant sequences before splitting the data into TR0 and TS0. |
| - augmented data: synthetic training examples were generated from bpRNA-new sequences by random mutation and structure prediction. |
| - PDB training data: high-resolution RNA structures from bpRNA and the PDB were used for fine-tuning/evaluation experiments; test sets TS1, TS2, and TS3 were filtered at 80% sequence identity. |
| - evaluation data: ArchiveII, TS0, bpRNA-new, and PDB test data were used for benchmark evaluation. |
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| ### Training Procedure |
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| - input representation: 16 outer-product channels following the MultiMolecule tokenizer order plus one hand-crafted pairing-score channel. |
| - objective: weighted binary cross entropy over base-pair contact maps. |
| - optimizer: Adam. |
| - training epochs: 100. |
| - batch size: 1. |
| - positive-class weight: 300. |
| - post-processing: constrained optimization with canonical/wobble pairing rules, sparsity shrinkage, and a 0.5 threshold. |
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| ## Citation |
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| ```bibtex |
| @article{fu2022ufold, |
| author = {Fu, Laiyi and Cao, Yingxin and Wu, Jie and Peng, Qinke and Nie, Qing and Xie, Xiaohui}, |
| title = {UFold: fast and accurate RNA secondary structure prediction with deep learning}, |
| journal = {Nucleic Acids Research}, |
| volume = {50}, |
| number = {3}, |
| pages = {e14}, |
| year = {2022}, |
| doi = {10.1093/nar/gkab1074} |
| } |
| ``` |
|
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| > [!NOTE] |
| > The artifacts distributed in this repository are part of the MultiMolecule project. |
| > If MultiMolecule supports your research, please cite the MultiMolecule project as follows: |
|
|
| ```bibtex |
| @software{chen_2024_12638419, |
| author = {Chen, Zhiyuan and Zhu, Sophia Y.}, |
| title = {MultiMolecule}, |
| doi = {10.5281/zenodo.12638419}, |
| publisher = {Zenodo}, |
| url = {https://doi.org/10.5281/zenodo.12638419}, |
| year = 2024, |
| month = may, |
| day = 4 |
| } |
| ``` |
|
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| ## Contact |
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| Please use GitHub issues of [MultiMolecule](https://github.com/DLS5-Omics/multimolecule/issues) for any questions or comments on the model card. |
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| Please contact the authors of the [UFold paper](https://doi.org/10.1093/nar/gkab1074) for questions or comments on the paper/model. |
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| ## License |
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| This model implementation is licensed under the [GNU Affero General Public License](license.md). |
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| For additional terms and clarifications, please refer to our [License FAQ](license-faq.md). |
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|
| ```spdx |
| SPDX-License-Identifier: AGPL-3.0-or-later |
| ``` |
