/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/ |
H A D | zscore.c | 177 int *AUGC = get_seq_composition(S, start, end, length); in get_zscore() local 180 average_free_energy = avg_regression(AUGC[0], in get_zscore() 181 AUGC[1], in get_zscore() 182 AUGC[2], in get_zscore() 183 AUGC[3], in get_zscore() 184 AUGC[4], in get_zscore() 189 double min_sd = minimal_sd(AUGC[0], AUGC[1], AUGC[2], AUGC[3], AUGC[4]); in get_zscore() 193 sd_free_energy = sd_regression(AUGC[0], AUGC[1], AUGC[2], AUGC[3], AUGC[4], d->sd_model); in get_zscore() 198 free(AUGC); in get_zscore()
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/utils/ |
H A D | svm_utils.c | 50 int *AUGC = get_seq_composition(S, 1, length, length); in get_z() local 53 average_free_energy = avg_regression(AUGC[0], in get_z() 54 AUGC[1], in get_z() 55 AUGC[2], in get_z() 56 AUGC[3], in get_z() 57 AUGC[4], in get_z() 63 sd_free_energy = sd_regression(AUGC[0], AUGC[1], AUGC[2], AUGC[3], AUGC[4], sd_model); in get_z() 72 free(AUGC); in get_z()
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/dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/ |
H A D | inverse_8h.tex | 19 …m This global variable points to the allowed bases, initially \char`\"{}\+AUGC\char`\"{}. It can b…
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H A D | group__inverse__fold.tex | 30 …m This global variable points to the allowed bases, initially \char`\"{}\+AUGC\char`\"{}. It can b…
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/bin/ |
H A D | RNAinverse.ggo | 18 … the search are read alternately from stdin.\nCharacters in the start sequence other than \"AUGC\"\
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/dports/biology/infernal/infernal-1.1.3/testsuite/ |
H A D | bug-i15.sto | 4063 …09_AE000751 GCUAACCGAAGAACCUUACCCGGGCUUGAC-AUGC-CGGGG--AGACUCC 4091 …:AE002280 GCAACGCGAAGGACCUUACCUGGGUUUGAC-AUGC-AUAUG--ACCGCGG 4121 … GCAACGCGAAGAACCUUACCAGGGCUUGAC-AUGC-AGGGA--AAUCUCG 4135 …g175128 GAUACGCGAAAAACCUUACCCGGGCUUGAC-AUGC-AUCAG--ACAGGCG 4147 …6657 GCAACGCGAAGAACCUUACCUGGGUUUGAC-AUGC-ACAGG--AUGCGUC 4149 …83920 GCAACGCGAAGAACCUUACCUGGGUUUGAC-AUGC-ACAGG--AUGCGUC 4153 …s.::Z83862 GCAACGCGAAGAACCUUACCUGGGUUUGAC-AUGC-ACAGG--ACGCGUC 4235 …74 GCUAAGCCAAGAACCUUACCAGGGCUUGAC-AUGC-CGGUG-GUACCUCC 4237 …01703 GCUAAGCCAAGAACCUUACCAGGGCUUGAC-AUGC-CGGUG-GUACCUCC 4241 …998 GCAACGCGAAGAACCUUACCAGGCCUUGAC-AUGC-UAGGG--AACCCGG [all …]
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H A D | Plant_SRP.sto | 494 AC190028.8/62420-62724 CUG.CAAC..CACAGU.CCACC.AUGGCC.UGGUGA..GCCUAG.AUGC.
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H A D | 3.4.12.rf.stk | 792 AF053589.1/90-279 ----UA-UGCUGGUG-UGUGU-GUGG-AUGC-UUU-GACA-GGCUU----
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H A D | 4.sto | 4007 AC190028.8/62420-62724 CUG.CAAC..CACAGU.CCACC.AUGGCC.UGGUGA..GCCUAG.AUGC.
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H A D | rnaseP-eubact.sto | 334 …----UGA-UCC-UG-ACG-------GUAA--------CGU-CAG--G-ACA-AGAUAAAUGAUGAGC-------AUGC-U---GA-------------…
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/dports/biology/infernal/infernal-1.1.3/tutorial/ |
H A D | Cobalamin.sto | 487 AL583923.1/215513-215333 ...AAAGG....CGAUGACG......AUGC..AGGAA.G.UC.G.G.UGC 491 CP000479.1/1283346-1283177 ...AUGA...........CG......AUGC..AGGAA.G.CC.G.G.UGC 492 BX248334.1/308192-308010 ...GUCAGG...CGAUGACG......AUGC..AGGAA.G.CC.G.G.UGA 494 BX842572.1/309867-309685 ...GUCAGG...CGAUGACG......AUGC..AGGAA.G.CC.G.G.UGA 3921 AE016853.1/3679925-3680123 .AUGC.CAGUCAGGAGACCUGCCGACCCGAUUCAACCAACU 3927 CP000058.1/3489261-3489461 .AUGC.CAGUCAGGAGACCUGCCGACCUGCUUCAACCCACU
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H A D | 5S_rRNA.sto | 701 AY544491.1/372-484 ..AUGC...GA.U.C.AU.ACC....AG.C.A.C.U...GA......... 707 AY544262.1/351-457 ....AUGC.GA.U.C.AU.ACC....AG.C.A.C.U...AA.........
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/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Perl/ |
H A D | RNA.pod | 272 C<inverse_fold> and C<inverse_pf_fold>, the default alphabet is "AUGC"
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/dports/biology/viennarna/ViennaRNA-2.4.18/man/ |
H A D | RNAlib.texi | 265 initially @code{"AUGC"}. It can be used to design sequences from reduced 1595 @c LocalWords: initially co noindent gmlRNA gml naview Bruccoleri struc AUGC
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/data/ |
H A D | rfam_seed_many_short.stk | 5319 AAVX01164741.1/393-468 UCCAAAA-CUGCAUACUUCUU-CAUAUGCCCAUA-UG-AA----AUGC-UUUGC-UAUGGAAUGUAAA… 5354 AEKZ01016876.1/452-379 GAUGCUG-UUCCGUGCUUCCU-UACUU-CCCAUA-GU-GG----AUGC-GACG--UAUGGAAUGUAAA… 27373 AC010057.7/174297-174216 GGU-UUU--UGUGAUGACAUAGCUAUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGCGUAA… 27374 AC010057.7/174076-173991 UUG-UUUUCAAUGAUGAUUUUCGAGUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAA… 27375 AAPP01019316.1/65510-65432 UUU-UGU-----GAUGAUAUAGCUAUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUUGUGUAA… 27376 AAPT01020539.1/126869-126954 AUU-AACGUAAUGAUGAGCUACGU-UUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAA… 27379 AADE01000021.1/111219-111300 UUGCGUUUUUGUGAUGAGAUAGCAA--UUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAA… 27380 AANI01017365.1/197782-197862 AAU-UACAUUGUGAUGAGCUAAGU-UUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAA… 27381 AAPU01011522.1/238759-238676 AAU-UGCUCUGUGAUGAGCUAAGC-UUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAA… 27382 AJ784351.1/2-80 UUU-U----GGUGAUGACAUAGCUAUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGCGUAA… [all …]
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H A D | rfam_seed_selected.stk | 660 AY544491.1/372-484 --AUGC---GA-U-C-AU-ACC----AG-C-A-C-U---GA----------A-GC-A----------C--CGG-… 679 AY544262.1/351-457 ----AUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-G----------C--CGG-…
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/dports/biology/viennarna/ViennaRNA-2.4.18/RNA-Tutorial/ |
H A D | tutorial.tex | 3173 % LocalWords: alifold alidot gsview RNASubopt mRNA Dalgarno AUGC Fp hetero kb
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