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language: rna
library_name: multimolecule
license: agpl-3.0
pipeline: rna-secondary-structure
pipeline_tag: other
tags:
  - Biology
  - 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{<{A<BB<A<B{CCAD<DDAABEDCEA)EDFBG])HG](ECCF[H}DCGG}HFDGH)IJK]>LMNabABE>FGLOJ))}](a(c(>[[MMbcdNaO>a}be{N{Oad{OLcaO>{cKad)](>[>bfgc)e}f)g(fgh}}gdiejdjh)kkcelb)f]}balgmmngdel.]nhom.o.oo.n.odh............................
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      GGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUAAAAAAAAA
  - example_title: 7SK small nuclear RNA
    output:
      text: >-
        .....................([{{.<....A..B.A.B..A....A..C......C.C...D..DEDEFECDDE)]}}(([>a{aa[<<EFbGa{A[GHA[bB)(B<<IHcHAB]AFBEI]FFFJBdGGDEI]HIGIJKFFHGIHKGHIK.HIK)}II>LHaMJKL][b[bcCK}d{{MNOPJ([{[BLCe))(]O.]>a><fd}ghefh(if(hg(bb<]gh}aa(i[)hgc[efAdAbOPei)]A)cjLjgc>bkihfdfce)ie{fikgjk)d]h>}}heaf()llkl]km>iianoaopoklgmpijhi..................
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      GGAUGUGAGGGCGAUCUGGCUGCGACAUCUGUCACCCCAUUGAUCGCCAGGGUUGAUUCGGCUGAUCUGGCUGGCUAGGCGGGUGUCCCCUUCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGCGCUCGGUCGAAGAGGACGACCAUCCCCGAUAGAGGAGGACCGGUCUUCGGUCAAGGGUAUACGAGUAGCUGCGCUCCCCUGCUAGAACCUCCAAACAAGCUCUCAAGGUCCAUUUGUAGGAGAACGUAGGGUAGUCAAGCUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGCAUGUGGCAGUCUGCCUUUCUUUU
  - example_title: telomerase RNA component
    output:
      text: >-
        .............................................((([.{<A[.B[{B<<([AB{{[((<CAA<DDB[[EBE(CF[{(GHAG<)HDBIECJFDE(EBJG)AI{EBJHKECBA)IFHIGKJDLJAK]J}HMFGCE)K}KLIM]NFEOJCEHKIMB)JCKDE)F]>IJaKaD]MJNIK]FEGH}LMN))b}(>KaNObMbHLNOPNcIaOcPbcOb]PdPMQ[dRc[BecMSeOdeR)>R(feTUaKNgMUd}effe]befRbP]hV{gh>{]<bShTTi)UfPeViiVjackgRkUdjalmkeWmnmheA)]l}i(}bi[k[Xmnojfg}>chpdnm{pohka)ipj(qek>rjjnkr]Cnstop>aulf)mro]i}gmhmjgrirobpisudbecjjnkkktvljtwvuump()xvk..noh..................
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC
  - example_title: vault RNA 2-1
    output:
      text: >-
        ..........................([{<AB..B..C.........)]}>abb([c()[)(({][<A)})(]])>...a............................
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      CGGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUUAUGCAA
  - example_title: brain cytoplasmic RNA 1
    output:
      text: >-
        ............................(((...[...........................................{<<<{A{AA{B[{{<<BA)))]((].....}.}..............>....)..)}>}.....}a}>>.a>ba.b....a.........................................
    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: >-
        ..............................(........................[[[.{[<.{[[{{[[<{{AAA<{A{<[B{<<A[C)((DD(ED(ED(EB((AB]CC])EDDDFEF]GEH}I]F}GGH>aH]}IHJJKLK}>].[LLLa>Lb)LML}NNc)OdMO..OP)QedNQ)O.>Pfg).d}RaSghhi>ITbjchjJb(e]cdBaf]kl}deCl]dB)}lgl]m)lfn]lo()am}enk>ohoppbiqbeqo(elcnrastd)([j)]i.()..........................
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AAUGUUCAAACACUUUGUGAAGCUCUGUUAGCUGAUGGUCUUGCUAAAGCAUUUCCUAGCAAUAUGAUGGUAGUCACAGAGCGUGAGCAAAAAGAAAGCUUAUUGCAUCAAGCAUCAUGGCACCACACAAGUGAUGAUUUUGGUGAGCAUGCCACAGUUAGAGGGAGUAGCUUUGUAACUGAUUUAGAGAAAUACAAUCUUGCAUUUAGAUAUGAGUUUACAGCACCUUUUAUAGAAUAUUGUAACCGUUGCUAUGGUGUUAAGAAUGUUUUUAAUUGGAUGCAUUAUACAAUCCCACAGUGUUAU
  - example_title: SARS coronavirus
    output:
      text: >-
        ..................................................((..[.....{......{(<([[{.[{[[A[{{<.A(ABA(AB{([(CCC.DE[A{[<F.{{{<......EEF.........GBA.CD..BEGC.D.ABB(C[D{<.)A].}>HECFGHHA<HIF.C.HI.[<DF<AIJAKHKL<KE.JL)M(EGILBAIHKMJ]KN]FLCE}>)K)F>JGMKOIHGJaF]N}JNLHMG>MOPI>QabL><RM}JaKNLOacN}aLabcb)OccadP])ebef>B>gCdeQ)]RfgSRhTiSCg(eUfjhfDSTf}fEgk}ghi>GGal<jlhai})aFaU]ajjAh]kUl]ljhki]k}mni]j}b)comcmcbddp>cqe))](rkdnels(sbrcdfjom}cncke}koteliaefspl>gggfbui)gh)hmunnhaoq()([m)]rtklu..............................
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AUGUUUAUUUUCUUAUUAUUUCUUACUCUCACUAGUGGUAGUGACCUUGACCGGUGCACCACUUUUGAUGAUGUUCAAGCUCCUAAUUACACUCAACAUACUUCAUCUAUGAGGGGGGUUUACUAUCCUGAUGAAAUUUUUAGAUCAGACACUCUUUAUUUAACUCAGGAUUUAUUUCUUCCAUUUUAUUCUAAUGUUACAGGGUUUCAUACUAUUAAUCAUACGUUUGACAACCCUGUCAUACCUUUUAAGGAUGGUAUUUAUUUUGCUGCCACAGAGAAAUCAAAUGUUGUCCGUGGUUGGGUUUUUGGUUCUACCAUGAACAACAAGUCACAGUCGGUGAUUAUUAUUAACAAUUCUACUAAUGUUGUUAUACGAGCAUGUAACUUUGAAUUGUGUGACAACCCUUUCUUUGCUGUUUCUAAACCCAUGGGUACACAGACACAUACUAUGAUAUUCGAUAAUGCAUUUAAAUGCACUUUCGAGUACAUAUCU
  - example_title: insulin
    output:
      text: >-
        .....................([{...<A...<.....BA.BB.......B.C.BDBDAADCDEABFECDFDEGGGC)(](}([>>{<{[([{[{{<F[G<EH<EGaDaHAF)(FbFcIFBG]A]EGHH(IE[)JBJJGDE]}{I>)KcLa([I){LKaKKbadLd]eaA]M)bK}>ALMe}e].Kde)bNfLgMbNgGN>)(dcb<h(acid}(bb(hii<d<j)A}]>kd)[fCeCagOefakOlOkPg(ek}jffOfj))gmhed>}k]klmlgiab)ncgn>loomglpn()f(g(oh)c>[o())]......................
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AUGGCCCUGUGGAUGCGCCUCCUGCCCCUGCUGGCGCUGCUGGCCCUCUGGGGACCUGACCCAGCCGCAGCCUUUGUGAACCAACACCUGUGCGGCUCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCCCUUGGCCCUGGAGGGGUCCCUGCAGAAGCGUGGCAUUGUGGAACAAUGCUGUACCAGCAUCUGCUCCCUCUACCAGCUGGAGAACUACUGCAACUAG
  - example_title: cyclin dependent kinase inhibitor 2A
    output:
      text: >-
        .......(.[...{{{..<.A..B...<)(](((.[..([[CDD(C[[DDCC[DAE(FAEGBBGFDCB}}FC}{GH{EH{I><I<DJAKL[GJEJFECIFJDGHFE{IGFKGKHGLKJLHKFCLLJHIIM)]KG}ME))LEM]F]})>IaJN(aL(aIJKMOAJAOKLbbPcMM[KcLdNePQL(ce>LRMNOePRf[{))MfP]SLIMJQSgJbORT]OPUfgcN}dh}])SO>{a<aV<eTg]ORVeiQjafAUbBBc)A)BAiiAjjBhfkllSgdUcTci]dReBAmUSRe)k(jm}Vih>]fl}gjfnhmc[lagd[)(o{loaf(kain{g(boebo{]h[jjd[kCaompn)plfmkmadqijliljmqrdgjbrrng)b.rk.}ssoppo}lk]s>l)}ptuctjv.qrms].]r.kimhs.kuul.tlu...vbv...........................
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AUGGAGCCGGCGGCGGGGAGCAGCAUGGAGCCUUCGGCUGACUGGCUGGCCACGGCCGCGGCCCGGGGUCGGGUAGAGGAGGUGCGGGCGCUGCUGGAGGCGGGGGCGCUGCCCAACGCACCGAAUAGUUACGGUCGGAGGCCGAUCCAGGUCAUGAUGAUGGGCAGCGCCCGAGUGGCGGAGCUGCUGCUGCUCCACGGCGCGGAGCCCAACUGCGCCGACCCCGCCACUCUCACCCGACCCGUGCACGACGCUGCCCGGGAGGGCUUCCUGGACACGCUGGUGGUGCUGCACCGGGCCGGGGCGCGGCUGGACGUGCGCGAUGCCUGGGGCCGUCUGCCCGUGGACCUGGCUGAGGAGCUGGGCCAUCGCGAUGUCGCACGGUACCUGCGCGCGGCUGCGGGGGGCACCAGAGGCAGUAACCAUGCCCGCAUAGAUGCCGCGGAAGGUCCCUCAGACAUCCCCGAUUGA
  - example_title: human papillomavirus type 16 E6
    output:
      text: >-
        ........................................(([(......{....<...A((.[{([<(AB([{(A<({[{[A(BB{[[[[CD<{({<EDDAE<A(E[)FF]GHIJC<FAGHH<B)BIBB)HCAKIDEF]G)HIJKL)]]MNOPQRSTUVWXYZ...YI(EGQMN}UFS.(BHOTHPZQOJXPVIGWKYHQW.X.>YaQQ>}TRY]{U.]R)>b)XaVJSb>Nbbcbdaee[[B..ffYg)W])ghhZg].hZ)DEi.]F}}jh.iG}j...ik..]jkl}}Im>nnamooppqnJqqrro)(b]J>pKabLqqqsccdCd][rsteee}[>sfutvf{gEwtauvg<hwbuwhx)BidfvaxMNdyz]wyy.Bjx.)xyzyAz].i)y))j]gk}..(zc>..}>e)...ea.ahil.(..b.bfmh.bin[)j]k..............................
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AUGCACCAAAAGAGAACUGCAAUGUUUCAGGACCCACAGGAGCGACCCAGAAAGUUACCACAGUUAUGCACAGAGCUGCAAACAACUAUACAUGAUAUAAUAUUAGAAUGUGUGUACUGCAAGCAACAGUUACUGCGACGUGAGGUAUAUGACUUUGCUUUUCGGGAUUUAUGCAUAGUAUAUAGAGAUGGGAAUCCAUAUGCUGUAUGUGAUAAAUGUUUAAAGUUUUAUUCUAAAAUUAGUGAGUAUAGACAUUAUUGUUAUAGUUUGUAUGGAACAACAUUAGAACAGCAAUACAACAAACCGUUGUGUGAUUUGUUAAUUAGGUGUAUUAACUGUCAAAAGCCACUGUGUCCUGAAGAAAAGCAAAGACAUCUGGACAAAAAGCAAAGAUUCCAUAAUAUAAGGGGUCGGUGGACCGGUCGAUGUAUGUCUUGUUGCAGAUCAUCAAGAACACGUAGAGAAACCCAGCUGUAA
  - example_title: NRAS proto-oncogene
    output:
      text: >-
        ..................(([({<<<{[ABAAAC.CC.DEBDFE.FGHIJK......))]])(((}}[[>>>[)(aaaa]bb]))c])deccfdghi(jefk)()()()......................
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      GGGGCCGGAAGUGCCGCUCCUUGGUGGGGGCUGUUCAUGGCGGUUCCGGGGUCUCCAACAUUUUUCCCGGCUGUGGUCCUAAAUCUGUCCAAAGCAGAGGCAGUGGAGCUUGAGGUUCUUGCUGGUGUGAA
  - example_title: amyloid beta precursor protein
    output:
      text: >-
        .......................((....[{<....................A<BCBCBD.EEFGCEGG((HI.(EJ)F)G)AI))]}>>(aabcbc[bcdeef(e{g))](ef}ghgi)g([)]ij.......................
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      GUCAGUUUCCUCGGCAGCGGUAGGCGAGAGCACGCGGAGGAGCGUGCGCGGGGGCCCCGGGAGACGGCGGCGGUGGCGGCGCGGGCAGAGCAAGGACGCGGCGGAUCCCACUCGCACAGCAGCGCACUCGGUGCCCCGCGCAGGGUCGCG
  - example_title: RUNX family transcription factor 1
    output:
      text: >-
        .............................................................((.[..[{..(<.[A{.{A[B{.<.ABB{C(C[)D(EE](E<E)F)GCHA)()]ID}HJ}{>I))a>]ab}(c}](J)JdKc](db)efe})}g>aaehih(eib(cjjjk)[)()]................
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      ACUUCUUUGGGCCUCAUAAACAACCACAGAACCACAAGUUGGGUAGCCUGGCAGUGUCAGAAGUCUGAACCCAGCAUAGUGGUCAGCAGGCAGGACGAAUCACACUGAAUGCAAACCACAGGGUUUCGCAGCGUGGUAAAAGAAAUCAUUGAGUCCCCCGCCUUCAGAAGAGGGUGCAUUUUCAGGAGGAAGCG
  - example_title: fragile X messenger ribonucleoprotein 1
    output:
      text: >-
        .......(.[(.{..({(<([{A.AB.CA..D.D.EF.B.DE.CEFE.DEG.)))])})(]}}[>a[a{a<AA[[<H({({b{b{c{d{{eB<cCAIB)CBIJI{Ad)JCJCI)(](](KIeeeJC[}K}}C}L)d(>e]}d(D]aE}(fD<faEF}bL)F])(c(}[gFc>bGGGc}>{M>a{c<M<d)]h)cei)}bf)jdkfig>}i.cjgf>il.)kjamglimj..e.............................
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      CUCAGUCAGGCGCUCAGCUCCGUUUCGGUUUCACUUCCGGUGGAGGGCCGCCUCUGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGCGGCGGUGACGGAGGCGCCGCUGCCAGGGGGCGUGCGGCAGCGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCUGGGCCUCGAGCGCCCGCAGCCCACCUCUCGGGGGCGGGCUCCCGGCGCUAGCAGGGCUGAAGAGAAG
  - example_title: MYC proto-oncogene
    output:
      text: >-
        ............................(([((.{{<.A{BCD{<{A{<{ABECBA<<BD(E[<AACDFGHBIGC(B[IDC(JJJJJJI)IECKLMD)]{<ABDMFHKD<BEAF)CBEGH]HIAGJIGBFHKJA}GK))D))](>a[a([>}[JLK>L}(KaMJL[MbbHGaLGHIJKLaNbO>OaPOJPcMdbbL>cKQb))Od(]>]N}efaPNd(aePcc[.dbQ}MgbhbfNc}gNijg>h}>k)ajgg]g<deahdbkc)]}dfcdhilijlj[kem[fem)](gjkknjl>hhngnlmn(knol]p(oohm)))iiijpjpqjkklqj.]ljmiopj.m..................
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      AACUCGCUGUAGUAAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGCCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUGAUCCCCCAGCCAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGCACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUAUUCUGCCCAUUUGGGGACACUUCCCCGCCGCUGCCAGGACCCGCUUCUCUGAAAGGCUCUCCUUGCAGCUGCUUAGACG
  - example_title: activating transcription factor 4
    output:
      text: >-
        .............((.[...{.<<.<.ABCDEFC{FBGGBBCCBHHGHDIHJ)E)((I(][[KIGLJG}I[KI[J}{M{>KaAAN(Kb(AAL>bL{AMMM[McLLLNLbMNc)O)PbQdRSTeQ)PP(OO]I]U}MNbBOSPcQ>]<cd][}{e)<f(gCaggCh()fiDbBg<agh<]ihjaa)AkAk)llBilEmnlmBlijnAooBlD}ohmp]>>)>(iopikcqaapbcbpjnmbk)qbq}.ldrsstmm>.aadeum.....n.............
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      CAUUUCUACUUUGCCCGCCCACAGAUGUAGUUUUCUCUGCGCGUGUGCGUUUUCCCUCCUCCCCGCCCUCAGGGUCCACGGCCACCAUGGCGUAUUAGGGGCAGCAGUGCCUGCGGCAGCAUUGGCCUUUGCAGCGGCGGCAGCAGCACCAGGCUCUGCAGCGGCAACCCCCAGCGGCUUAAGCCAUGGCGCUUCUCACGGCAUUCAGCAGCAGCGUUGCUGUAACCGACAAAGACACCUUCGAAUUAAGCACAUUCCUCGAUUCCAGCAAAGCACCGCAAC
  - example_title: Human GPI protein p137
    output:
      text: >-
        ..........................................................([((...(((.(.{([{({.(<<[A{B<<.A.BCBABBBCBDCBDCE.ED.FEGF.BFFF)GADGECHHCGIJCDKJKHEIKHLFFGGH(LHBG]))}[{[>[aab)b)bc]d]bef]cc}cfdg)][ecghdghaebf}gM<g(hgN<fEGNhb[cibOh))ijbk])dId)b)}]Dl>>)>]l>>(ajkeffce)}gbmfghennkdi.o..............................
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      UUUUUAAAAGGAAAAGAUACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUUUGAAAGGCACCAGUAUGUGUUUUAGAUUGAUUUAAAUGUUUCAUUUAAAUCACGGACAGUAGUUUCAGUUCUGAUGGUAUAAGCAAAACAAAUAAAACGUUUAUAAAAGUUGUAUCUUGAAACACUGGUGUUCAACAGCUAGCAGCUUAUGUGAUUCACCCCAUGCCACGUUAGUGUCACAAAUUUUAUGGUUUAUCUCCAGCAACAUUUCUCUAGUACUUGCACUUAUUAUCUGAAUUC
  - example_title: nucleophosmin 1
    output:
      text: >-
        ..............................(([.........{.{<(.AAB...[C{D<<AD.[A<{.(CE({.A<D(((.BF[{<A<FBAB)EBBCDDEFD[B{EF)<EFG(A<H)GCGH)]HIDG}D]>[}>{HJEaHIJIJKFK><JIFKGJKFLGHa[))bK(MNKNcbAO]M]L}LdK>I)efI)J]gdL]a)M][b)(b}}[cd[>Mfg>CN)d(d}(O>]ah[eaff>gghgijFabOiij[baekilDk}e)>lci>}ha]b)kdalcmcj]dkjfmlghdj]mdmneffo()oeni]nfhkfkokjh...................
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      GAAAAUAGUUUAAACAAUUUGUUAAAAAAUUUUCCGUCUUAUUUCAUUUCUGUAACAGUUGAUAUCUGGCUGUCCUUUUUAUAAUGCAGAGUGAGAACUUUCCCUACCGUGUUUGAUAAAUGUUGUCCAGGUUCUAUUGCCAAGAAUGUGUUGUCCAAAAUGCCUGUUUAGUUUUUAAAGAUGGAACUCCACCCUUUGCUUGGUUUUAAGUAUGUAUGGAAUGUUAUGAUAGGACAUAGUAGUAGCGGUGGUCAGACAUGGAAAUGGUGGGGAGACAAAAAUAUACAUGUGAAAUAAAACUCAGUAUUUUAAUAAAGUAGCACGGUUUCUAUUGA
  - example_title: superoxide dismutase 1
    output:
      text: >-
        ............................................(([{<A<ABABCCDDD{D{EBF{<{{FD{GE<AE)G)(]([[F[[B[A[FGA<DHGBAHHGGHIIJKLEMCFMFF}LMK..N)MM.MN]..O.]P.P.O...}>.].a.].......P.....)..(........QR}SQ>T(}..}(a>P}.a.R}>b{a.b]abbcc.{..d.Q.defef.f.eQ]..fgg.h...gh>aic...baj........kkdgdhlmdmeld)noo}pm[)qpp)mqffhg}pqrm]qrngimstf............................................
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      ACAUUCCCUUGGAUGUAGUCUGAGGCCCCUUAACUCAUCUGUUAUCCUGCUAGCUGUAGAAAUGUAUCCUGAUAAACAUUAAACACUGUAAUCUUAAAAGUGUAAUUGUGUGACUUUUUCAGAGUUGCUUUAAAGUACCUGUAGUGAGAAACUGAUUUAUGAUCACUUGGAAGAUUUGUAUAGUUUUAUAAAACUCAGUUAAAAUGUCUGUUUCAAUGACCUGUAUUUUGCCAGACUUAAAUCACAGAUGGGUAUUAAACUUGUCAGAAUUUCUUUGUCAUUCAAGCCUGUGAAUAAAAACCCUGUAUGGCACUUAUUAUGAGGCUAUUAAAAGAAUCCAAAUUCAAACUAAA
  - example_title: hemoglobin subunit alpha 2
    output:
      text: >-
        ..............(((....[.....(.[{[{<A..A.AA.BCD)EE]}]>abc)d]}[))aa(a)ee...]....................................
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      CUGGAGCCUCGGUAGCCGUUCCUCCUGCCCGCUGGGCCUCCCAACGGGCCCUCCUCCCCUCCUUGCACCGGCCCUUCCUGGUCUUUGAAUAAAGUCUGAGUGGGCAGCA
  - example_title: BRAF proto-oncogene
    output:
      text: >-
        .................................................([...)]..(.((([{..<([(A{<ABC{D{{(<[<A(BACAA{<<<(<<EFA<BC{DEFGHIJB[AHDACKBCD{EBEFBIBFGFEB)JGCDE)(JFGHI)J]JKLMN})]GJK)M}}{)HLO)F>]L<][))NO(Ma([bb[cPdbe}L[LNbbLcd[DOQMN{OPf{DQfDRgahDM>g)S(OG]{]NhD(THGG<))iHj}eT]>I[>>H[e)a}UUb>cddfS>(}b}kd>dg(B)cUl]C)>(l]mhj]dadgl}bP>gdlafkhge)}mnfeEh]lanablj[}fmiF>oamcg)}g>ompcbnach.h]pnqri(djoeinssootjt)ufjef(kupuq())...................
    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

Pre-trained model for RNA secondary structure prediction using an image-like sequence representation and a U-Net.

Disclaimer

This is an UNOFFICIAL implementation of UFold: fast and accurate RNA secondary structure prediction with deep learning by Laiyi Fu, Yingxin Cao, Jie Wu, Qinke Peng, Qing Nie, and Xiaohui Xie.

The OFFICIAL repository of UFold is at uci-cbcl/UFold.

The MultiMolecule implementation is a direct PyTorch port of the original U-Net architecture and feature construction.

The team releasing UFold did not write this model card for this model so this model card has been written by the MultiMolecule team.

Model Details

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.

Model Specification

Num Parameters (M)	FLOPs (G)	MACs (G)
8.64	188.29	93.81

FLOPs and MACs are computed with multimolecule.utils for one 600 nt sequence.

Usage

The model file depends on the multimolecule library. You can install it using pip:

pip install multimolecule

RNA Secondary Structure Pipeline

import multimolecule
from transformers import pipeline

predictor = pipeline("rna-secondary-structure", model="multimolecule/ufold")
output = predictor("GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCUCA")

PyTorch Inference

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

To run the original constrained post-processing loop:

output = model(**inputs, use_postprocessing=True)
contact_map = output.postprocessed_contact_map

Training Details

UFold was trained for RNA secondary structure prediction from annotated contact maps and base-pairing rules.

Training Data

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.

Training Procedure

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.

Citation

@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}
}

The artifacts distributed in this repository are part of the MultiMolecule project. If you use MultiMolecule in your research, you must cite the MultiMolecule project.

License

This model is licensed under the GNU Affero General Public License.

For additional terms and clarifications, please refer to our License FAQ.

SPDX-License-Identifier: AGPL-3.0-or-later

multimolecule
/

ufold

UFold

Disclaimer

Model Details

Model Specification

Links

Usage

RNA Secondary Structure Pipeline

PyTorch Inference

Training Details

Training Data

Training Procedure

Citation

License