first summer commit

models/RF00168.stockholm.txt

+# STOCKHOLM 1.0
+
+#=GF AC   RF00168
+#=GF ID   Lysine
+#=GF DE   Lysine riboswitch
+#=GF AU   Wickiser JK, Barrick JE, Breaker RR
+#=GF SE   Wickiser JK, Barrick JE
+#=GF SS   Published; PMID:12787499
+#=GF GA   30.00
+#=GF TC   30.10
+#=GF NC   29.70
+#=GF TP   Cis-reg; riboswitch;
+#=GF BM   cmbuild -F CM SEED
+#=GF CB   cmcalibrate --mpi CM
+#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
+#=GF DR   SO; 0000035; riboswitch;
+#=GF RN   [1]
+#=GF RM   12787499
+#=GF RT   Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis
+#=GF RT   and Other Bacteria.
+#=GF RA   Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR
+#=GF RL   Cell 2003;113:577-586.
+#=GF RN   [2]
+#=GF RM   14523230
+#=GF RT   The L box regulon: Lysine sensing by leader RNAs of bacterial lysine
+#=GF RT   biosynthesis genes.
+#=GF RA   Grundy FJ, Lehman SC, Henkin TM
+#=GF RL   Proc Natl Acad Sci U S A 2003;100:12057-12062.
+#=GF RN   [3]
+#=GF RM   14597663
+#=GF RT   An mRNA structure in bacteria that controls gene expression by binding
+#=GF RT   lysine.
+#=GF RA   Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR
+#=GF RL   Genes Dev 2003;17:2688-2697.
+#=GF RN   [4]
+#=GF RM   14627808
+#=GF RT   Regulation of lysine biosynthesis and transport genes in bacteria: yet
+#=GF RT   another RNA riboswitch?.
+#=GF RA   Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS
+#=GF RL   Nucleic Acids Res 2003;31:6748-6757.
+#=GF CC   Riboswitches are metabolite binding domains within certain messenger RNAs
+#=GF CC   that serve as precision sensors for their corresponding targets.
+#=GF CC   Allosteric rearrangement of mRNA structure is mediated by ligand binding,
+#=GF CC   and this results in modulation of gene expression. This family includes
+#=GF CC   riboswitches that sense lysine [1] in a number of genes involved in lysine
+#=GF CC   metabolism, including lysC [3].
+#=GF WK   Lysine_riboswitch
+#=GF SQ   47
+
+
+U00006.1/98763-98567       CAGGCCAGAAGAGGC-GCGUUG-CCC-A--A--GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
+J03294.1/2297-2476         GGUGAAGAUAGAGGU-GCGAAC-UUC-AAGA--GUA--UGCCUUUGGAGA-------AAGAUGGAUUCUGUG---AAAAAGG-CU-GAAAGG-GGA-GCGUCGCCGAAGCAAAUAAAACCCCAUCG------GUAUUAUU-UGCUGGCCGUG-CAUU--GAAUAAAUGUAAGGCUGUCAAGAAA--UCA------------------------------------------------------------UUUUCUUGG-AGGGCUAUCUCGUUG
+AF269536.1/680-500         AAUAGAGUUAGAGGUUGCAUUA-UUA-AUGA--CUA--ACUUAUCAGAAGUCGU---AUGGGACAUGUGUUG---A--AUAA-GU-GAAAGG-UAA-U-AAUGCCGAAAUGAUGUUAUUUC-CAUA-A----AUUAGCAU-UGUGAAGUUGG-UUGAA-CAAUAAAAACAUCACAACCACGAAU--GCU--------------------------------------------------------------UUCUUCA-AUAUUUAUUUGAAUU
+AF270308.1/2156-2331       AAUAGAGUUAGAGGUUGCAUUA-UUA-AUGA--CUA--ACUUAUCAGAAGUCGU---AUGGGACAUGUGUUG---A--AUAA-GU-GAAAGG-UAA-U-AAUGCCGAAAUGAUGUUAUUUC-CAUA-A----AUUAGCAU-UGUUGGGACAA-CUUUC-GAAUAGAAGUUGUACUGUCACU-----UUA----------------------------------------------------------------UGUGA-UGUGCUACCUUAUAU
+M93419.1/332-511           AGUGAAGAUAGAGGU-GCGAAC-UUC-AUCA--GUA--AAAGCUUGGAGAA------GAAUGAGCUUCAAUG---AAAAGCU-UU-GAAAGG-GAACG-UUCGCCGAAGUGAAGAAAAA---CUCAUU----UUUUUCUU-UGCUGGUCCUG-CAUU--UAAGAGAUGCCGGAUUGUCAAGGCGG-UGC-------------------------------------------------------------CGCCUUGG-AGAGCUAUCUCACUG
+AF306669.1/1019-1194       AUAUUUUGAUGAGGC-GCAUCA-AUC-AUGA--GUA--AAGUUUAGAUUAC------UGUCUGCUAACAG------CUAAAU-UU-GAAAGG-GUG-C-GAUGCCGAAGC-AAUUAUAAU--AGCA-G----UUAUAAUU-UGUUGGACUUUUUGGU--UAAGAGCUGAGAGUUUGUCAUUAUU--UAA------------------------------------------------------------AAAUAAUGG-AGUGCAUCACUUGUA
+X00008.1/296-492           CAGGCCAGAAGAGGC-GCGUUG-CCC-A--A--GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUAAG-GGGGCUGAAU-CCC-CUGGGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
+X15196.1/270-75            GCAGCCAGAAGAGGC-GCGUUG-CCA-A-----GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
+AL591976.1/186683-186486   UGGUGAGGUAGAGGUUGCGAGA-UGC-ACUA--GUA--AUUUUUUCGAGGCGAA---ACAAAGACGCCGACG---ACAAAGA-AU-GAACAG-GUU-G-AUCGCCGAAGUGACUAUUUUCU-CUUU-GUUUAGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGGGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
+AL596166.1/112469-112272   UGGUGAGGUAGAGGUUGCGAGA-UGC-ACUA--GUA--AUUUUUUCGAGGCGAA---ACAAAGACGCCAAUG---ACAAAAA-AC-GAACAG-GUU-A-AUCGCCGAAGUGACUAUUUUUU-CUUU-GUAUCGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGAGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
+AAMR01000029.1/5147-5324   AUCGCACGUAGAGGC-GCAAUU-AUA-AAAA--GUA--GUUUUCGUU----------GGGGUGAUGCCAAUG---AGCGGGA-AU-GAAAGG-UCU-A-AUUGCCGAAGUAAAUUGUAU---AUCU------AAGCAAUU-UGCUGGGGUUG-UGCU--CAAUAGGUACAACACUGCCAUAGUC--UUAAUUUU-------------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
+CP000002.3/2878377-2878198 GGUGAAGAUAGAGGU-GCGAAC-UUC-AAGA--GUA--GGCUUGAUGAGGA------AGAUGGAUUCCGAUG---AAGAAAG-CC-GAAAGG-GGA-GCGUCGCCGAAGCGGGGAAAAAUC-CACU-C----GUUUUUCC-UGCUGGCUUUA-CAUU--GAAUAAAUGUGAGGCUGUCAAGAAA--UCA-------------------------------------------------------------UUUCUUGG-AGAGCUAUCUCGUUG
+BX950851.1/4451556-4451748 CAAGCCAGAAGAGGC-GCGUCG-CCC-AG----GUA--AGAUAUCGGAGG-------AACCGUAAUCCGCUG---AUGAUAU-CC-GAGGGG-GAG-C-GACGCCGAGAUGCGGUGAAAUU-CGGC------UUUCACCC-UAUCGACUACA-GAGGCUGAAU-CCUCUG-GGUUGUCACCGGA--UUCGUCCUGAUGGACGUCCA-------------------------------------------GCAAGGUGG-AGCGCUUCUGGGUGU
+EF419299.1/175-1           AAAAGAGUUAGAGGUUGCGUCU-UUA-AUUA--GUA--ACACUUCAGAAGUUAUU--AAGGAACGUGUGUUG---A--AAGU-GU-GGAAGG-UAA-A-GAUGCCGAAAUGAAUGAUACC--CUUA-A----UUAUCAUU-UGUUGGGACAG-UUAUC-GAAUAGAAACUGUACUGUCACA-----AUU----------------------------------------------------------------UGUGA-UGUGCUACC-GACGG
+CP000046.1/1759610-1759435 AAUUGAGUUAGAGGUUGCAUGU-UUA-AUUA--GUA--ACUUGUCAGAAGUAUUU--AUGGUACAUAAGUUG---A--ACAA-GU-GAAAGG-UAA-A-GAUGCCGAAAUAGAUAUAAACC-AUAA------AUUAUAUC-UAUUGGGACAG-UUUUC-GAAUAGGAACUGUACUGUCACA-----GAA----------------------------------------------------------------UGUGA-UGUGCUACCUUAUAU
+BA000037.2/1373591-1373770 UAUCGACGUAGAGGC-GCAAUG-GUA-AAGA--GUA--ACUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GAAAGG-UAU-CCAUUGCCGAAGUGAAUUGCAU---AUCA------AAGCAGUU-UGCUGGGGUUG-CAUCC-GAAA-GGAACAACACUGCCAUAGUA--UUUAAUGUA------------------------------------------------------UAACUAUGG-AGCGCUACUGUAGGU
+CP000647.1/4829910-4829675 AUUGCCAGAAGAGGU-GCGUUG-CCC-AG----GUAA-CCGUAUUGGA---------GGAACCAGUCCGGGG---AAGAUAC-GU-GAGGGG-GAG-C-AACGCCGAGGUGAAAGAGCGUCUGGUC-A----CGCUCC-U-CGCCGGCCACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AACGUUCGCAGUCGGGCGUUUCAUACCCGAACACCUCAGCGCCCAAAGCGGUGAGUCGGGUCUACAAGGUGG-AGCACUUCUGGGUGA
+BA000004.3/1819757-1819575 AGUGAGGAUAGAGGU-GCAAAA-ACC-AAGA--GUA--CACAAUUGGAGGA------GAAUGAGAUCCGUUG---AGAAUUG-UG-GAAAGG-GGA-A-UUUGCCGAAGC---UGGAAGAAUCUCA-U----GUUCUGAA-GGCUGGUUCUG-UAUU--AAAUAAAUACAGAACUGUCAUAUAGCGGAUGUU---------------------------------------------------------GCUAUAUGG-AGGGCUAUCUCACGC
+ABCF01000065.1/4547-4725   AGUGGUGAUAGAGGU-GCGGAC-UUUCAUCA--GUA--GAUGCUUCGAGGA------GUAUGGGCUCUUAUG---AAGGGUA-UC-GAAAGG-GAA-A-UUCGCCGAAGUGGAAGCAGGCU-CAUA------UCUGUUUG-CGCUGGUUCUG-UGUU--UAAGAGAUGCAGGAUUGUCAAGAUUA-ACA--------------------------------------------------------------GUCUUGG-AGAGCUAUCUCACGU
+AE017143.1/992934-993104   ACAAAUUGUAGAGGU-GCAAAU-CCG-AUAA--GUA--UUUCUUCU-----------GAGUGGAAAGCGAUG---AAGGGGA-AG-GAAAGG-CGU-A-UUUGCCGAAAUCAAUUAAGC---GUCA------UCUUAGUU-GGUUGGGGUCG-UUGCC-GAAA-GGGACGACACUGUCGUAAUU--CAA-------------------------------------------------------------UAUUACGG-AGUGCUACUAUUAGG
+CP000002.3/3366091-3365915 UAGUGAGGUAGAGGUUGCGCGG-AUG-AUGA--GUC--GCAUGUGUGAGG-------CUGAUGGGGCCGAUG---AUCAUAU-GC-AAAAGG-CAU-C-AGCGCCGAAGCAUAAGGAAGCC-AUUC------AUUCUUUA-UGCUGGGUCUG-CAUU--GAAUAAGUGCAGGACUGCCGCGGGU--AUU--------------------------------------------------------------CCCGCGG-AGGGCUAUCCGGAGA
+CP000029.1/981298-981477   AGAUUUUGAUGAGGC-GCAUCA-AUC-AUGA--GUA--AACUUUAGAUAAU------UUGUCUGCUAACAAU---UAUAGAG-UU-AAAAGG-GUG-A-GAUGCCGAAAUGAUUCAUAAU--AGCA-G----UUAUGAAU-CGUUGGACUUAAUGGU--UAAGAGCUAUAAGUUUGUCAUUAUU--AUU------------------------------------------------------------AAAUAAUGG-AGUGCAUCACUUGUA
+AAWP01000069.1/5541-5721   UAUUGCCGUAGAGGU-GCAGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGA-GGAUUGCCGAAGUAGGUGGCCU---AUCG------AAGCCACU-UGCUGGGGUUG-UCUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUUUACAUU-----------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
+AAKK02000085.1/12844-12662 UGUUGCCGUAGAGGC-GCGGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGAAG-AUUGCCGAAGUAAGUAACUC---AUCA------AAGUUACU-UGCUGGGGUUG-UAUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUAUUCACAUU---------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
+CP000416.1/1669940-1669758 UCGAAUAGAAGAGGC-GCGACC-AAC-AAGA--GUC--GCUUUCCGGAGA-------UGGGUCACAUUGCUG---AUGGAAG-GU-UAAAGG-GGC-G-GUCGCCGAAAUUUACGCAUUUU-GACC-G----GAUGCGUG-GGUUGGGUCCU-GGUU--GAACAAGUCAGGGACUGUCGCAGUCA-AAUAAU---------------------------------------------------------CGGCUGCGG-GGCGCUUUCAACGAU
+AM263198.1/783761-783564   UGGUGAGGUAGAGGUUGCAAGA-UUC-ACAA--GUA--AUUUUUUAGAAGCGAA---ACAAAGACGCUGAUG---ACAAAGA-AU-GAACAG-GAU-G-AUUGCCGAAGUGACUAUUUUCU-CUUU-GUUUAGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGAGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
+AP006716.1/1558409-1558233 AGAAAUUGAUGAGGC-GCAUCA-AUC-AUCA--GUA--UAUAUUAGAU---------AAACUGUCUGCAACA---GCUAAUA-UA-GAAAGG-GUG-C-GAUGCCGAAAUGAAUCAUAAU--CGCA-G----CUAUGAUU-UGUUGGACUUUGUGGU--UAAGAGCUGAAAGUUUGUCAUUAUU--AUU------------------------------------------------------------UAAUAAUGG-AGUGCAUCACUUGUA
+ABDQ01000005.1/49327-49153 AACUAAGAUAGAGGU-GCGAGA-UUU-AAGA--GUA--GUAUUAUG-----------GAGUUAAGUGCUAAG---AAGUAAU-AA-GAAAGG-AAA-U-UUCGCCGAAGCUUAUAGAUAAUACUUU-A----AUGCUAUU-UGCUGGGAUUA-CAUA--AAAUAUAUGUAAGACUGUCACAAAU--AAA-------------------------------------------------------------GUUUGUGG-AGAGCUAUUAUUUUA
+AE016827.1/1325416-1325239 UACACAUGUAGAGGU-GCGAAU-AUU-AUAA--GUA--UUUUUCCA-----------GAGUGGAUAACAAUG---AAGGAAA-UU-GAAAGG-AAU-A-UUUGCCGAAAUCAGUUAAGC---GUCA------UCUUAACU-GGUUGGUAACG-UCACC-GAAA-GGAACGUUACUGCCAUAGUC--AUUUUUGAU------------------------------------------------------UAACUAUGG-AGCGCUACUCGUGGG
+CP000569.1/516240-516411   ACAAAUCGUAGAGGU-GCAAAU-CCG-AUAA--GUA--CUUUUUCU-----------GAGUGGAGAACGAGG---AGGAAAA-AG-GAAAGG-CGU-A-UUUGCCGAAAUCAGUUAAGC---GUCA------UCUUAAUU-GGUUGGGGUCG-UUACC-GAAA-GGGACGACACUGUCGUAAUC--CUU------------------------------------------------------------GUAUUACGG-AGUGCUACUGCUAGG
+BA000031.2/1190723-1190903 UGUUGCCGUAGAGGC-GCAGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGAAG-AUUGCCGAAGUAAGUCGUAU---AUCA------AAACGCCU-UGCUGGGGUUG-UAUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUUUACAUU-----------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
+CP000425.1/2337129-2337310 CACAUCGAUAGAGGUCGCAACU-GAU-AUGA--AUC----UACGCCGAGU-------UGGAGCACAACAAAG---ACGCGUA-UUAGAGGGGGAGA-A-GUUGCCGAAAGAAUUUUGAC---GCUC-A----G-CAAAGU-UCUUGGGCUAG-UGAG--GAAAACUCACUAGACUGUCGCAAAUGGUUAAGA---------------------------------------------------------ACCAUGCGG-AGGGCUAUUCGUUCA
+AASA01000017.1/10332-10501 ACAAAUUGUAGAGGU-GCGAAU-UCA-AUAA--GUA--UUUCUUCU-----------GAGUGGAAAACGAUG---AAGGGGA-AG-GAAAGG-UGA-A-UUUGCCGAAAUCAAUUAAGC---GUCA------UCUUAAUU-GGUUGGGGUCG-UUGUC-GAAA-GAAACGACACUGUCGUAGUA--AAU--------------------------------------------------------------GCUACGG-AGUGCUACUGUUAGG
+AP008934.1/1400599-1400421 AGGUUUUGAUGAGGC-GCAUCA-AUC-AUUA--GUA--AAGAUUAGAAGA-------AUCUGACUGCUAGCA---GCUAAUU-UU-GAAAGG-GUG-A-GAUGCCGAAACGGUUAUAAU---AGCA-G----CUUAUAACAUGUUGGACUUUAUGGU--UAAGAGCUAAGAGUCUGUCAUUAUU--UUA------------------------------------------------------------AGAUAAUGG-AGUGCAUCACUUGUA
+AAOX01000015.1/22460-22639 AGUGAAGGUAGAGGU-GCAAAC-UUC-AUCA--GUA--AAAGCUUGGAGAA------AGAUGAGUUUCCGUG---AAAAGCU-UU-GAAAGG-GAAUG-UUUGCCGAAGAAAAGGAAGUCU-CAUU------UCUUUCUU-UUCUGGUCCUG-UAUU--GAAUAAAUACUGGAUUGUCAAGACA--GCG------------------------------------------------------------CCGUCUUGG-AGAGCUAUCUCACUG
+AL009126.3/3421348-3421169 CAGUGAGGUAGAGGUUGCGCGG-AUG-AUGA--GUC--ACACAUGCUA---------GGCUGACAGGGGCUGUUAAACAUGU-GU-AAAAGG-CAU-C-AGCGCCGAAGUGUGGAGAAAGCCGAUC------CUUCUCUA-UGCUGGGACUG-UAUCU-GAAUAAGUGCAGGACUGCCGCGUGC--UUU--------------------------------------------------------------UUCGCGG-AGGGCUAUCCGGAGA
+AE008691.1/719320-719498   CGCAUAAAUAGAGGA-GCUGCC-AAGCAU----GUA--UUUGGCGAGGUGUUAAGGAGAAGAACCUCCAAUA---CUCGCUG-AA-GAA-GG-UUU-G-GCUGCCGAAAGGGUGAGCUUG--UUCU-U----GAGCUCAU-CCUUGGUGGUA-AAC-A-CAAA--GUUUACCACUGUCAUGGGA--CCU--------------------------------------------------------------CCCAUGA-AGCGCUAUUUAUGCA
+AE004439.1/1026545-1026371 UACUUGUGUAGAGGA-GCGAUC-ACU-AUAA--GUA--UUUUUUCU-----------GAGUGGAUAACGAAG---AGGAAAA-AG-GAAAGG-AGU-G-ACCGCCGAAAUCAAUUGAAA---GUCA------UUUUGAUU-GGUUGGUGGCG-UAUUC-GAAA-GGAACGUCAUUGUCAUAGUC--UUUUUU---------------------------------------------------------AAACUAUGG-AGCGCUACUGGUUGG
+CP000436.1/843556-843727   UACAUAUGUAGAGGU-GCGGCU-GUU-AUAA--GUA--AUUUUUU------------GAGUGGAUAACGAUG---A-AAAAA-AU-GAAAGG-AAU-A-GUUGCCGAAAUCAAUUAAAA---GUCA------UUUUAAUU-GGUUGGGGGCG-UAUUC-GAAA-GAAACGUCACUGUCAUAGUA--UUU-AU---------------------------------------------------------CCACUAUGG-AGCGCUACUGGUUAG
+CP001186.1/1355449-1355630 CUCAAAGGUAGAGGCCGCGAUA-GGA-AAGA--GUA--AGCUAUGGGAGAU------UUAAUGGAAUCUGUG---AUCAUAGGUU-GAAAGG-GAC-U-AUUGCCGAAAUAUAAGAAUAAC-CAUC-U----UAUUCAUA-UAUUGGGACUA-CAUU--GAAUAAAUGUAGUACUGUCAUAAGA--UUU------------------------------------------------------------AUUUUAUGG-AGAGCUAUUUGGAGA
+AE005176.1/2276232-2276414 CACAUCGAUAGAGGUCGCAACU-GAU-AUGAAUCUACGCCGAGUUGG----------AGCACAACAAAGACG---CGUAUUU-AG-AGGAGG-AGA-G-GUUGCCGAAAGAAUUUUGUU---GCUC------AGCAAGGU-UCUUGGGCUAG-UGAG--AAAAACUCACUAGACUGUCGCAAAUG-GUUAAUA--------------------------------------------------------ACCAUGCGG-AGGGCUAUUCGUUCA
+CP000923.1/1076332-1076143 AGGUGAGGUAGAGGC-GCGGGUUAUC-AAGA--GUA--GUAUACCAGAGGU------AUUUAAGGGCCGAUG---AAGGUAU-AU-GAAAGG-GAU-G-CUCGCCGAAGC-GCGUAAAUUCCUUAA-A----GUUUACGC-AGCUGGGCCUA-UGCC--GAAUAGGUAUAGGACUGUCACUGGA--GGUUUCCCGAGC---------------------------------------------------CUUCAGUGA-AGAGCUAUCUCGCUA
+AE008691.1/1930427-1930616 AGGUGAGGUAGAGGC-GCGGGU-CAUCAAGA--GUA--ACAUGCCAGAGG-------UGUUAAGGGCCGAUG---AAGGUGU-GU-GAAAGG-GGU-G-CCCGCCGAAGC-GCGUAAACUUCCUUAAG----GUUUACGC-AGCUGGGCCUA-UGCC--GAACAGGUAUAGGACUGUCACUGAAG-GCUCCCCAGGC----------------------------------------------------CUUCAGUGG-AGAGCUAUCUCGCUA
+CP000826.1/4955718-4955911 CAAGCCAGAAGAGGU-GCGUCG-CCC-AG----GUA--GAGUGUCAGAGG-------AGCCGUUGUCCAAUG---ACGGCGC-UU-GAGGGG-GAG-C-GACGCCGAGGUAAGGUGAUGUG-CGGC------AUUCAUCG-UAUCGACUACA-GGGGCUGAAU-CCCCUG-AGUUGUCACCAGGG-AUUGUCCGUAGGGGCAAUCA-------------------------------------------GCAAGGUGG-GGCGCUUCUGGGUGU
+AL935263.2/928916-929097   AUCGAAAGAAGAGGAUGCGGUU-AAC-AAUA--GUA--GCCGGCUGGAAGU------GGGUCACCACUUAUG---AAGGUCA-GU-GAACGG-GGC-A-ACCGCCGAAAUCGAUGGAUCAGUGACC------GAUUCAUC-CGUUGGGCCUU-GGUU--GAAUAAAUCAUGGACUGUCGCAGCUA-GAA------------------------------------------------------------UAGUUGCGG-GGCGCUAUCGACGAU
+AALE02000022.1/49827-50019 UAAGCCAGAAGAGGU-GCGUCG-CCC-AG----GUA--AAGUGUCAGAGG-------AGCCGUGAUCCGCUG---AAGACAU-UC-GAGGGG-GAG-C-GACGCCGAGACACGGUGAUUUC-GGCC-------AUCAGCG-UGUCGACUGCA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGU--GCCGUUCCUUUAGGGCGGUCA------------------------------------------ACAAGGUGG-AGCGCUUCUGGGUGU
+FQ670178.1/927246-927070   UACAAAAGUAGAGGC-GCAAUU-AUU-AUAA--GUA--UUUUUUCA-----------GAGUGGAUAACGAAG---AAGAAAA-AA-GAAAGG-AAU-A-GUUGCCGAAAUCAAAUAAAA---GUCG------UUUUGUUU-GGUUGGUGGCG-UGCUC-GAAA-GGGGCGACACUGUCAUAGUU--UUUCUGAU-------------------------------------------------------UAACUAUGG-AGUGCUACGGUUGUU
+#=GC SS_cons               :::::((((((,,,,.<<<<<<.<<<.----..---..<<<<<<<<____......._______________..._>>>>>>.>>.------.>>>.>.>>>>>,,,<<<<<<<<<<<<__.____._....>>>>>>>>.>>>><<<<<<<.<<<<_.____.>>>>>>>>>>>,<<<<<<<_.._______........................................................__>>>>>>>.,,,,)))))):::::
+#=GC RF                    aaugacgguAGAGGU.GCgucc.cuc.AugA..GUA..acuuuucuGAgg.......ggaugaaaucCgaUG...Aagaaaa.gu.GAAAGG.gag.g.gacGCCGAagugaguggaccuc.guua.a....gguccacu.cgcuGGccccg.uggcC.GAAu.gccacggggCUGuCAccgua..uuugUuc........................................................acacggUGg.AGcGCUaccggguga
+//

models/RF02540.stockholm.txt

 inary files /dev/null and b/models/RF02540.stockholm.txt differ

models/analyzw_rna3dmotif.py

+import pickle
+
+
+
+
+
+modules = pickle.load(open("all3dmotif_graphs.cPickle",'rb'))
+sig_g=[]
+good_mods = []
+n = 0
+for i in range(len(modules)):
+    length = len(modules[i][0])
+    if length>20 :
+        good_mods.append(i)
+        gr = modules[i][0]
+        pdbs = [(modules[i][1][mod_id][0],list(modules[i][0][mod_id].nodes)) for mod_id in range(len(modules[i][1]))]
+        sig_g.append({"l_graphs":gr,"names":pdbs})
+    if length>20:
+        n=n+1
+
+print(n)
+pickle.dump(sig_g,open("best3dmotif_graphs.cPickle",'wb'))

models/cleanup_subgraphs.py

+import pickle
+from matplotlib import pyplot as plt
+import networkx as nx
+
+modules = pickle.load(open("rna3dmotif_one_of_each_graph.cPickle",'rb'))
+interesting = [2, 8, 9, 14, 20, 28, 36, 59, 113, 127, 133, 150, 162, 194, 195]
+
+for i in interesting:
+    g0 = modules[i][0]
+    pos = nx.circular_layout(g0)
+    nx.draw_networkx_nodes(g0,pos,nodelist=g0.nodes,node_color='red',node_size=500)
+    nx.draw_networkx_edges(g0,pos,edgelist=g0.edges(),edge_color='green',width=2)
+    labels={}
+    elabels = {}
+    for i in g0.nodes():
+        labels[i] = i
+    nx.draw_networkx_labels(g0,pos,labels)
+    for i in g0.edges():
+        elabels[i]=g0.get_edge_data(*i)['label']
+    nx.draw_networkx_edge_labels(g0,pos,elabels)
+    plt.show()
+
+
+"""
+def get_seq(g):
+    seq = ""
+    for i in list(g.nodes):
+        seq = seq + str(i)
+    return seq
+
+def module_seqs(ind):
+    seqs = []
+    gs = modules[ind]
+    for graph in gs:
+        seq = get_seq(graph)
+        if seq not in seqs:
+            seqs.append(seq)
+    return(len(seqs))
+
+def get_seq_variation():
+    n_seqs = []
+    for i in range(len(modules)):
+        n = module_seqs(i)
+        n_seqs.append(n)
+    return n_seqs
+
+ns = get_seq_variation()
+goods = []
+for i in range(len(ns)):
+    g = modules[i][0]
+    #print(list(g.edges(data=True)))
+    if not any( (x[2]["label"]!="b53" and x[2]["label"]!="cWW") for x in list(g.edges(data=True))):
+        continue
+    if ns[i]>8:
+        goods.append(i)
+
+print(goods)
+print(len(goods))
+"""

models/module_to_infernal.py

+import networkx as nx
+from matplotlib import pyplot as plt
+import pickle
+modules = pickle.load(open("rna3dmotif_one_of_each_graph.cPickle",'rb'))
+aln_list = pickle.load(open("rna3dmotif_aligned_modulegraphs.cPickle",'rb'))
+PDBs = pickle.load(open("rna3dmotif_PDB_names.cPickle",'rb'))
+PDBs = pickle.load(open("rna3dmotif_PDB_positions.cPickle",'rb'))
+
+def get_seq(g,aln):
+    addresses = list(g.nodes)
+    seq = ""
+    for j in range(min(addresses),max(addresses)+1):
+        #print(j)
+        if j in addresses:
+            #print(list(g.nodes))
+            index = list(g.nodes).index(j)
+            #print(list(g.nodes(data=True))[index])
+            nuc = list(g.nodes(data=True))[index][1]['nuc']
+            seq = seq + nuc
+        else:
+            seq = seq + '-'
+    return seq
+
+for i in range(len(modules[0])):
+    g = modules[0][i]
+    aln = aln_list[i]
+    s = get_seq(g,aln)
+    print(s)

models/results.txt

+GOOD COLUMNS [[868], [869], [870], [871], [872], [873], [877]]
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+STRUCTURE SEQUENCE:  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+PURE RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+PURE RFAM SEQUENCE :  ['G', 'A', 'U', 'U', 'A', 'U', 'A']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'U', 'U', 'U', 'C']
+PURE RFAM SEQUENCE :  ['U', '-', '-', 'A', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'C', 'A', 'G', 'A']
+PURE RFAM SEQUENCE :  ['-', '-', 'G', 'A', 'G', 'A', '-']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'A', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'G', 'A', 'A', 'A', 'U']
+PURE RFAM SEQUENCE :  ['G', 'A', 'G', 'A', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['C', 'U', 'U', 'C', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'C']
+PURE RFAM SEQUENCE :  ['G', 'A', 'G', 'A', 'A', 'C', 'C']
+PURE RFAM SEQUENCE :  ['-', '-', 'G', 'A', 'A', 'A', '-']
+PURE RFAM SEQUENCE :  ['C', '-', 'U', 'U', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'A', 'U', 'C', 'A', 'U', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['-', 'C', 'A', 'C', 'A', 'A', '-']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['A', '-', 'U', 'U', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['U', '-', 'C', 'G', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['G', 'A', 'G', 'U', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['C', 'U', 'U', 'C', 'A', 'C', 'A']
+PURE RFAM SEQUENCE :  ['G', 'A', 'U', 'U', 'A', 'U', 'U']
+PURE RFAM SEQUENCE :  ['G', 'G', 'A', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['-', 'C', 'G', 'A', 'A', 'A', '-']
+PURE RFAM SEQUENCE :  ['C', '-', 'G', 'A', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['C', 'U', 'U', 'U', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['U', '-', '-', 'G', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'C', 'A', 'U', 'C']
+PURE RFAM SEQUENCE :  ['A', '-', 'G', 'U', 'A', 'G', 'G']
+PURE RFAM SEQUENCE :  ['U', '-', 'A', 'G', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['G', 'A', 'U', 'C', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['G', 'U', 'C', 'U', 'A', 'C', 'C']
+PURE RFAM SEQUENCE :  ['U', '-', 'U', 'U', 'A', 'A', 'U']
+PURE RFAM SEQUENCE :  ['C', 'U', 'U', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['U', 'U', 'U', 'A', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['U', '-', 'G', 'C', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['-', '-', '-', '-', '-', '-', '-']
+PURE RFAM SEQUENCE :  ['C', 'U', 'U', 'U', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['U', '-', '-', 'U', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'U', 'A', 'C', 'G']
+PURE RFAM SEQUENCE :  ['-', 'G', 'U', 'U', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['U', '-', 'U', 'A', 'U', 'G', 'G']
+PURE RFAM SEQUENCE :  ['C', 'U', 'U', 'U', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['C', 'U', 'G', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'A', 'A', 'A', 'A', '-']
+PURE RFAM SEQUENCE :  ['U', 'U', 'U', 'A', 'C', 'A', 'A']
+PURE RFAM SEQUENCE :  ['U', 'G', 'U', 'U', 'A', 'U', '-']
+PURE RFAM SEQUENCE :  ['A', 'G', 'U', 'C', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'C', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['C', 'U', 'U', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'U', 'A', 'G', 'U']
+PURE RFAM SEQUENCE :  ['-', '-', 'G', 'A', 'A', 'A', '-']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'A', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'G', 'A', 'A', 'C', 'G']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'C', 'A', 'C', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['U', 'U', 'U', 'A', '-', '-', 'A']
+PURE RFAM SEQUENCE :  ['-', 'U', 'C', 'A', 'A', 'A', '-']
+PURE RFAM SEQUENCE :  ['C', '-', '-', 'U', 'A', 'U', 'A']
+PURE RFAM SEQUENCE :  ['G', 'A', 'U', 'A', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['C', 'C', 'G', 'A', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['-', '-', 'G', 'G', 'A', 'A', '-']
+PURE RFAM SEQUENCE :  ['G', 'U', 'G', 'U', 'G', 'U', 'U']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['U', 'U', 'U', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['U', '-', 'U', 'U', 'A', 'U', 'U']
+PURE RFAM SEQUENCE :  ['-', 'C', 'A', 'A', 'A', 'A', '-']
+PURE RFAM SEQUENCE :  ['G', 'A', 'U', 'A', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['G', 'A', 'G', 'A', 'A', 'C', 'G']
+PURE RFAM SEQUENCE :  ['A', 'U', 'U', 'U', '-', '-', 'G']
+PURE RFAM SEQUENCE :  ['G', 'C', 'U', 'U', 'A', 'A', 'U']
+PURE RFAM SEQUENCE :  ['G', 'A', 'G', 'C', 'A', 'U', 'G']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'G', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['U', '-', '-', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'C', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['A', 'U', 'U', 'A', 'A', 'A', 'U']
+PURE RFAM SEQUENCE :  ['C', 'U', 'A', 'G', 'A', 'A', 'G']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'U', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'U', 'U', 'A', 'U']
+PURE RFAM SEQUENCE :  ['G', 'A', 'U', 'C', 'A', 'U', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'C', 'A', 'C', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'U', 'U', 'A', 'C', 'C']
+PURE RFAM SEQUENCE :  ['G', 'U', 'A', 'U', 'C', 'U', 'U']
+
+==============================================================
+
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+STRUCTURE SEQUENCE:  ['C', 'G', 'G', 'C', 'G', 'A', 'G']
+RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'A', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'A', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['U', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'U', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']
+PURE RFAM SEQUENCE :  ['G', 'G', 'C', 'G', 'A', 'G', 'C']

models/rna3dmotif_parse.py

+import os
+import networkx as nx
+import matplotlib
+from matplotlib import pyplot as plt
+import networkx.algorithms.isomorphism as iso
+import operator
+import pickle
+def compare_graphs(g1,g2):
+    em = iso.generic_edge_match('label',["cWW","tWW","cWS","tWS","cWH","tWH","cHH","tHH","tHW","cHW","cHS","tHS","cSW","tSW","cSH","tSH","cSS","tSS","c++","t++","c--","t--","b53"],operator.eq)
+
+    isof = nx.is_isomorphic(g1,g2,edge_match=em)
+    return isof
+
+def make_align_graph(g1):
+    corr_edges = []
+    g0 = nx.DiGraph()
+    g0.add_nodes_from(g1.nodes())
+    g0.add_edges_from(g1.edges())
+    pos = nx.spring_layout(g0)
+    nx.draw_networkx_nodes(g0,pos,nodelist=g1.nodes(),node_color='red',node_size=500)
+    nx.draw_networkx_edges(g0,pos,edgelist=g1.edges(),edge_color='red',width=2)
+    labels={}
+    elabels = {}
+    for i in g0.nodes():
+        labels[i] = i
+    nx.draw_networkx_labels(g0,pos,labels)
+    for i in g1.edges():
+        elabels[i]=g1.get_edge_data(*i)['label']
+    nx.draw_networkx_edge_labels(g0,pos,elabels)
+    plt.show()
+
+os.chdir('DESC')
+#print(os.listdir('.'))
+tot = len(os.listdir('.'))
+z=0
+graphs = []
+IDs = []
+bob = nx.DiGraph()
+for i in os.listdir('.'):
+    if 'desc' in i:
+        #print(i)
+        z = z+1
+        if z%100==0:
+            print("doing number "+str(z)+" of "+str(tot))
+        g = nx.DiGraph()
+        with open(i,'r') as desc :
+            lines = desc.readlines()
+            if len(lines)<2:
+                continue
+            nodestuff = lines[1].split(" ")
+            #print(nodestuff)
+            for n in nodestuff:
+                if len(n)>0:
+                    if n[0].isdigit():
+                        node_n = n[:-2]
+                        nt = n[-1]
+                        g.add_node(int(node_n),nuc=nt)
+            for line in range(2,len(lines)):
+                bp = lines[line].split("---")
+                #print (bp)
+                p1 =bp[0][4:8].replace(" ","")
+                p2 =bp[2][2:7]
+
+                #if '(' in p2.split():
+                 #   p2.replace("(","")
+                #rint(p1,p2)
+                #p1 = "".join([s for s in p1_.split() if s.isdigit()])
+                #p2 = "".join([s for s in p2_.split() if s.isdigit()])
+                #print(p1,p2)
+                #print(p1_,p2_)
+                interaction = bp[1][1:4]
+                orientation = bp[1][5]
+                #print(p1,p2,interaction,orientation)
+                if orientation=='s':
+                    continue
+                elif interaction=="C/C":
+                    g.add_edge(int(p1),int(p2),long_range=False ,label='b53')
+                elif interaction=="+/+" or interaction=="-/-":
+                    bond = orientation + "WW"
+                    g.add_edge(int(p1), int(p2), long_range= False, label=bond)
+                else:
+                    bond = orientation + interaction[0]+interaction[2]
+                    g.add_edge(int(p1), int(p2), long_range=False, label= bond)
+        #nx.draw(g)
+        #print("GRAPH")
+        #print(g.nodes(data=True))
+        #print(g.edges(data=True))
+        #for i in g.edges():
+         #   print(i, g.get_edge_data(*i))
+        if len(graphs)==0:
+            graphs.append([g])
+            IDs.append([i[:-5]])
+        else:
+            found = False
+            kk=0
+            #print("GOT HERE")
+            while kk < len(graphs) and found==False:
+                if compare_graphs(g,graphs[kk][0])==True:
+                    graphs[kk].append(g)
+                    IDs[kk].append([i[:-5]])
+                    found=True
+                kk = kk+1