8 #define WORDLENGTH 2 /* default word length in stem candidates (SCs) */
12 // the parameter trained by maximazing the sps of tRNA
13 //#define MULTISCORE 9.870619 //multiple score with the constant.
14 //#define MULTIRIBOSUM 0.452626 //multiple ribosum_score with the constant
15 //#define MULTIPENALTY 24.263776 //multiple penalty with the constatnt
16 //#define MULTISTACKING 45.208927 //multiple stacking energy with the constatnt
19 #define MULTIRIBOSUM 1
20 #define MULTIPENALTY 3.1
21 #define MULTISCORE 3.7
22 #define MULTISTACKING 0.1
23 #define MULTIDELTASCORE 9.4
24 #define MULTIDELTASTACKING 8.6
27 #define MULTIRIBOSUM 1
28 #define MULTIPENALTY 1.1162
29 #define MULTISCORE 0.53299
30 #define MULTISTACKING 4.25669
31 #define MULTIDELTASCORE 1.17805
32 #define MULTIDELTASTACKING 4.2016
34 // new CRF DATA 550 sigma 1
36 #define MULTIRIBOSUM 1
37 #define MULTIPENALTY 1.82294
38 #define MULTISCORE 0.250631
39 #define MULTISTACKING 2.35517
40 #define MULTIDELTASCORE 1.1781
41 #define MULTIDELTASTACKING 2.45417
44 #define MULTIRIBOSUM 1
45 #define MULTIPENALTY 0.478054
46 #define MULTISCORE 1.36322
47 #define MULTISTACKING 4.96635
48 #define MULTIDELTASCORE 1.14239
49 #define MULTIDELTASTACKING 7.32992
51 // CRF DATA 900 sigma 1
53 #define MULTIRIBOSUM 1
54 #define MULTIPENALTY 2.28364
55 #define MULTISCORE 0.00945681
56 #define MULTISTACKING 2.25357
57 #define MULTIDELTASCORE 1.02201
58 #define MULTIDELTASTACKING 2.21293
62 #define RNAMATCHAA 506159
63 #define RNAMATCHAT 359916
64 #define RNAMATCHAG 451319
65 #define RNAMATCHAC 390720
66 #define RNAMATCHTT 398658
67 #define RNAMATCHTG 377069
68 #define RNAMATCHTC 378456
69 #define RNAMATCHGG 554695
70 #define RNAMATCHGC 419950
71 #define RNAMATCHCC 479030
72 #define GAPPENALTY 190947
73 #define GAPEXTENTIONPENALTY -118817
76 #define RNAMATCHAA 2.22
77 #define RNAMATCHAT -1.39
78 #define RNAMATCHAG -1.46
79 #define RNAMATCHAC -1.86
80 #define RNAMATCHTT 1.65
81 #define RNAMATCHTG -1.74
82 #define RNAMATCHTC -1.05
83 #define RNAMATCHGG 1.03
84 #define RNAMATCHGC -2.48
85 #define RNAMATCHCC 1.16
86 //#define GAPPENALTY 9.42 // 3default linear gap penalry in RNA sequence alignment
87 //#define GAPPENALTY 9.18743
88 //#define GAPPENALTY 5.00
89 //#define GAPEXTENTIONPENALTY 7.15
90 //#define GAPEXTENTIONPENALTY 9.62003
93 #define GAPEXTENTIONPENALTY 2.5
94 //#define GAPPENALTY 8.08875
95 //#define GAPEXTENTIONPENALTY 3.89655
97 #define REFINEMENTREPS 0
99 #define BASEPROBTHRESHOLD 0.01
100 #define BASEPAIRCONST 6
101 #define BANDWIDTH 500
102 #define USERFOLD false
104 extern float RNA_Match_AA;
105 extern float RNA_Match_AT;
106 extern float RNA_Match_AG;
107 extern float RNA_Match_AC;
108 extern float RNA_Match_TT;
109 extern float RNA_Match_TG;
110 extern float RNA_Match_TC;
111 extern float RNA_Match_GG;
112 extern float RNA_Match_GC;
113 extern float RNA_Match_CC;
114 extern float RNA_Gap_Penalty;
115 extern float RNA_Gap_Extension;
117 extern int numIterativeRefinementReps;
118 extern bool PostProcessAlignment;
119 extern int scsLength;
120 extern float BaseProbThreshold;
121 extern float BasePairConst;
123 #endif /*__SCARNA_HPP__*/