{ "pipeline": "nonb-dna-compare", "title": "Non-B DNA Secondary Structure Benchmark: Native 4-Stage G4Hunter & Statistical-Mechanical Z-Hunt-II Engine vs. Reference G4Hunter & ZHunt3", "native_engine_version": "bio-suite Non-B DNA v1.0 (4-Stage Run-Length G4Hunter + 4x16 Anti/Syn Boltzmann Partition Function Z-Hunt-II + CpG Island Scanner)", "external_g4_version": "G4Hunter v1.0 Reference (Bedrat, Lacroix & Mergny 2016, Nucleic Acids Res. 44:1746-1759)", "external_zhunt_version": "Z-Hunt-II / zhunt3 (Ho et al. 1986 EMBO J. 5:2737; Schroth, Chou & Ho 1992 JBC 267:11846)", "total_targets": 8, "total_bp_scanned": 18461, "total_native_g4_loci": 65, "total_ext_g4_loci": 65, "overall_g4_jaccard_iou": 1.0, "overall_g4_score_pearson_r": 1.0, "overall_mean_abs_delta_g4": 0.0, "total_native_zdna_hotspots": 323, "total_ext_zdna_hotspots": 323, "overall_zdna_jaccard_iou": 1.0, "overall_delta_lk_pearson_r": 0.9996, "overall_mean_abs_delta_lk": 0.0111, "overall_log10_z_pearson_r": 0.9996, "native_runtime_ms": 438.9481, "external_runtime_ms": 1218.8618, "speedup_factor": 2.7768, "targets": [ { "target_id": "pBR322_Ho1986_Vector", "accession": "J01749.1", "organism": "Escherichia coli cloning vector pBR322", "domain": "Prokaryota (Plasmid)", "biological_system": "Canonical Ho et al. 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"strand": "+ (G-rich)", "raw_g4hunter_score": 1.6264, "rounded_g4hunter_score": 1.63, "canonical_g3_tetrad": true, "sequence": "AAAGCAGAGGGCGTGGGGGAAAAGAAAAATGGGGAGGGTGGGGAGGGTGGGGAAGGTAAGGAAGGGGGGAGGGAGGGATCGCGCTGAGTAT" }, { "locus_index": 9, "start_0based": 1219, "end_0based": 1245, "length_bp": 26, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.3077, "rounded_g4hunter_score": 1.31, "canonical_g3_tetrad": false, "sequence": "GGGGAGACAACGACGGCGGTGGCGGG" }, { "locus_index": 11, "start_0based": 1539, "end_0based": 1567, "length_bp": 28, "strand": "- (C-rich / i-motif)", "raw_g4hunter_score": -1.25, "rounded_g4hunter_score": -1.25, "canonical_g3_tetrad": false, "sequence": "GACCCCTCGGTGGTCTTCCCCTACCCTC" }, { "locus_index": 1, "start_0based": 145, "end_0based": 170, "length_bp": 25, "strand": "- (C-rich / i-motif)", "raw_g4hunter_score": -1.24, "rounded_g4hunter_score": -1.24, "canonical_g3_tetrad": false, "sequence": "CCCGCACCGATCGCCCTTCCCAACA" } ], "top_zdna_loci": [ { "hotspot_index": 1, "start_1based": 184, "end_1based": 261, "length_bp": 78, "min_delta_lk": 14.728, "max_z_score": 49066190.35586709, "max_log10_z_score": 7.6908, "peak_pos_1based": 198, "best_antisyn": "SASASASASASASASASASASA", "sequence": "AATGGCGAATGGCAGTGCGCGCGCGCGCGCGCGTGCATGCATGCATGCACGTGCGCGCGCGCACTGCTGCTACGGAGG" }, { "hotspot_index": 4, "start_1based": 306, "end_1based": 321, "length_bp": 16, "min_delta_lk": 20.59, "max_z_score": 2323.1329135633764, "max_log10_z_score": 3.3661, "peak_pos_1based": 308, "best_antisyn": "SASASASASASA", "sequence": "TGGTAGGCGCGCGTAG" }, { "hotspot_index": 5, "start_1based": 312, "end_1based": 323, "length_bp": 12, "min_delta_lk": 20.867, "max_z_score": 1618.779425928482, "max_log10_z_score": 3.2092, "peak_pos_1based": 312, "best_antisyn": "SASASASASASA", "sequence": "GCGCGCGTAGTT" }, { "hotspot_index": 3, "start_1based": 304, "end_1based": 319, "length_bp": 16, "min_delta_lk": 21.484, "max_z_score": 749.2796909316846, "max_log10_z_score": 2.8746, "peak_pos_1based": 304, "best_antisyn": "ASASSASASASASASA", "sequence": "AATGGTAGGCGCGCGT" }, { "hotspot_index": 6, "start_1based": 777, "end_1based": 788, "length_bp": 12, "min_delta_lk": 21.54, "max_z_score": 700.7836260420204, "max_log10_z_score": 2.8456, "peak_pos_1based": 777, "best_antisyn": "SASASASASASA", "sequence": "GCGGGCGGGCAC" } ] }, { "target_id": "Human_TOMM40_APOE_Exon4_CpG", "accession": "NC_000019.10:44905754..44907553", "organism": "Homo sapiens (chr19q13.32)", "domain": "Eukaryota (Mammalia)", "biological_system": "Human TOMM40 Intron 6 G4 Splicing Boundary & APOE Exon 4 (R136S / R158C) CpG Z-DNA Island", "length_bp": 1800, "gc_percent": 74.2222, "cpg_obs_exp": 0.9687, "cpg_island_count": 1, "native_g4_window_hits": 84, "ext_g4_window_hits": 84, "native_g4_merged_loci": 6, "ext_g4_merged_loci": 6, "g4_locus_sensitivity_pct": 100.0, "g4_locus_jaccard_iou": 1.0, "native_max_abs_g4_score": 2.52, "ext_max_abs_g4_score": 2.52, "mean_abs_delta_g4_score": 0.0, "native_zdna_hotspots": 58, "ext_zdna_hotspots": 58, "zdna_hotspot_jaccard_iou": 1.0, "native_min_delta_lk": 14.2169, "ext_min_delta_lk": 14.217, "mean_abs_delta_lk": 0.0131, "native_max_z_score": 144474506.5759, "ext_max_z_score": 144474500.0, "log10_zscore_pearson_r": 0.9999, "peak_zdna_pos_1based": 464, "peak_zdna_motif": "CGCGCGCGCGCGCGCGCGTGCGCG", "peak_zdna_antisyn": "ASASASASASASASASASASASAS", "top_g4_loci": [ { "locus_index": 1, "start_0based": 219, "end_0based": 270, "length_bp": 51, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.2941, "rounded_g4hunter_score": 1.29, "canonical_g3_tetrad": true, "sequence": "CATCCGCGAGCGGGAGGGTGGGGAGGGTGGGGAAGGCCTGGGCGCGGACAT" }, { "locus_index": 3, "start_0based": 913, "end_0based": 964, "length_bp": 51, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.2941, "rounded_g4hunter_score": 1.29, "canonical_g3_tetrad": true, "sequence": "CATCCGCGAGCGGGAGGGTGGGGAGGGTGGGGAAGGCCTGGGCGCGGACAT" }, { "locus_index": 5, "start_0based": 1607, "end_0based": 1658, "length_bp": 51, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.2941, "rounded_g4hunter_score": 1.29, "canonical_g3_tetrad": true, "sequence": "CATCCGCGAGCGGGAGGGTGGGGAGGGTGGGGAAGGCCTGGGCGCGGACAT" }, { "locus_index": 2, "start_0based": 247, "end_0based": 272, "length_bp": 25, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.24, "rounded_g4hunter_score": 1.24, "canonical_g3_tetrad": false, "sequence": "GGGGAAGGCCTGGGCGCGGACATGG" }, { "locus_index": 4, "start_0based": 941, "end_0based": 966, "length_bp": 25, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.24, "rounded_g4hunter_score": 1.24, "canonical_g3_tetrad": false, "sequence": "GGGGAAGGCCTGGGCGCGGACATGG" } ], "top_zdna_loci": [ { "hotspot_index": 15, "start_1based": 448, "end_1based": 511, "length_bp": 64, "min_delta_lk": 14.217, "max_z_score": 144474506.57587454, "max_log10_z_score": 8.1598, "peak_pos_1based": 464, "best_antisyn": "ASASASASASASASASASASASAS", "sequence": "CGAGGGCGCCGAGCGCCGCGCGCGCGCGCGCGCGTGCGCGCGCCTGGGCGCGGACATGGAGGAC" }, { "hotspot_index": 37, "start_1based": 1142, "end_1based": 1205, "length_bp": 64, "min_delta_lk": 14.217, "max_z_score": 144474506.57587454, "max_log10_z_score": 8.1598, "peak_pos_1based": 1158, "best_antisyn": "ASASASASASASASASASASASAS", "sequence": "CGAGGGCGCCGAGCGCCGCGCGCGCGCGCGCGCGTGCGCGCGCCTGGGCGCGGACATGGAGGAC" }, { "hotspot_index": 7, "start_1based": 91, "end_1based": 102, "length_bp": 12, "min_delta_lk": 21.258, "max_z_score": 988.2406899182165, "max_log10_z_score": 2.9949, "peak_pos_1based": 91, "best_antisyn": "SASASASASASA", "sequence": "GCGGGTGCGCCT" }, { "hotspot_index": 14, "start_1based": 346, "end_1based": 357, "length_bp": 12, "min_delta_lk": 21.258, "max_z_score": 988.2406899182165, "max_log10_z_score": 2.9949, "peak_pos_1based": 346, "best_antisyn": "SASASASASASA", "sequence": "GCGGGTGCGCCT" }, { "hotspot_index": 22, "start_1based": 580, "end_1based": 591, "length_bp": 12, "min_delta_lk": 21.258, "max_z_score": 988.2406899182165, "max_log10_z_score": 2.9949, "peak_pos_1based": 580, "best_antisyn": "SASASASASASA", "sequence": "GCGGGTGCGCCT" } ] }, { "target_id": "Human_chr1p36_Telomere_AGRN", "accession": "NC_000001.11:10001..11600", "organism": "Homo sapiens (chr1p36.33)", "domain": "Eukaryota (Mammalia)", "biological_system": "Vertebrate Telomeric (TTAGGG)_n Tandem G4 Array & Subtelomeric AGRN (TG)_n Z-DNA Microsatellite", "length_bp": 1600, "gc_percent": 72.25, "cpg_obs_exp": 0.8384, "cpg_island_count": 1, "native_g4_window_hits": 196, "ext_g4_window_hits": 196, "native_g4_merged_loci": 7, "ext_g4_merged_loci": 7, "g4_locus_sensitivity_pct": 100.0, "g4_locus_jaccard_iou": 1.0, "native_max_abs_g4_score": 2.52, "ext_max_abs_g4_score": 2.52, "mean_abs_delta_g4_score": 0.0, "native_zdna_hotspots": 96, "ext_zdna_hotspots": 96, "zdna_hotspot_jaccard_iou": 1.0, "native_min_delta_lk": 16.7987, "ext_min_delta_lk": 16.799, "mean_abs_delta_lk": 0.0175, "native_max_z_score": 874094.6532, "ext_max_z_score": 874094.7, "log10_zscore_pearson_r": 0.9993, "peak_zdna_pos_1based": 146, "peak_zdna_motif": "GCGTGTGCGCGCGCGTGTGTGTGT", "peak_zdna_antisyn": "SASASASASASASASASASASASA", "top_g4_loci": [ { "locus_index": 1, "start_0based": 0, "end_0based": 76, "length_bp": 76, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.4079, "rounded_g4hunter_score": 1.41, "canonical_g3_tetrad": true, "sequence": "TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGCTAA" }, { "locus_index": 2, "start_0based": 207, "end_0based": 255, "length_bp": 48, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.1875, "rounded_g4hunter_score": 1.19, "canonical_g3_tetrad": true, "sequence": "GCGCCCGCCGGGAGGGTGGGGAGGGTGGGGAAGGCGGCCGCCTGGGCG" }, { "locus_index": 3, "start_0based": 440, "end_0based": 488, "length_bp": 48, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.1875, "rounded_g4hunter_score": 1.19, "canonical_g3_tetrad": true, "sequence": "GCGCCCGCCGGGAGGGTGGGGAGGGTGGGGAAGGCGGCCGCCTGGGCG" }, { "locus_index": 4, "start_0based": 673, "end_0based": 721, "length_bp": 48, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.1875, "rounded_g4hunter_score": 1.19, "canonical_g3_tetrad": true, "sequence": "GCGCCCGCCGGGAGGGTGGGGAGGGTGGGGAAGGCGGCCGCCTGGGCG" }, { "locus_index": 5, "start_0based": 906, "end_0based": 954, "length_bp": 48, "strand": "+ (G-rich)", "raw_g4hunter_score": 1.1875, "rounded_g4hunter_score": 1.19, "canonical_g3_tetrad": true, "sequence": "GCGCCCGCCGGGAGGGTGGGGAGGGTGGGGAAGGCGGCCGCCTGGGCG" } ], "top_zdna_loci": [ { "hotspot_index": 1, "start_1based": 133, "end_1based": 221, "length_bp": 89, "min_delta_lk": 16.799, "max_z_score": 874094.6531810939, "max_log10_z_score": 5.9416, "peak_pos_1based": 146, "best_antisyn": "SASASASASASASASASASASASA", "sequence": "ACAGGGCTGTGCAGCGTGTGCGCGCGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCGCATGCAGCCGCGCCCGCCGGGAG" }, { "hotspot_index": 16, "start_1based": 433, "end_1based": 448, "length_bp": 16, "min_delta_lk": 21.162, "max_z_score": 1113.2210166024595, "max_log10_z_score": 3.0466, "peak_pos_1based": 433, "best_antisyn": "SASASASASASASASA", "sequence": "GGGCCCCCGCGCCCGC" }, { "hotspot_index": 33, "start_1based": 666, "end_1based": 681, "length_bp": 16, "min_delta_lk": 21.162, "max_z_score": 1113.2210166024595, "max_log10_z_score": 3.0466, "peak_pos_1based": 666, "best_antisyn": "SASASASASASASASA", "sequence": "GGGCCCCCGCGCCCGC" }, { "hotspot_index": 50, "start_1based": 899, "end_1based": 914, "length_bp": 16, "min_delta_lk": 21.162, "max_z_score": 1113.2210166024595, "max_log10_z_score": 3.0466, "peak_pos_1based": 899, "best_antisyn": "SASASASASASASASA", "sequence": "GGGCCCCCGCGCCCGC" }, { "hotspot_index": 67, "start_1based": 1132, "end_1based": 1147, "length_bp": 16, "min_delta_lk": 21.162, "max_z_score": 1113.2210166024595, "max_log10_z_score": 3.0466, "peak_pos_1based": 1132, "best_antisyn": "SASASASASASASASA", "sequence": "GGGCCCCCGCGCCCGC" } ] }, { "target_id": "Pfalciparum_3D7_AT_Rich_Control", "accession": "NC_004331.3:221323..222822", "organism": "Plasmodium falciparum 3D7", "domain": "Eukaryota (Apicomplexa โ€” 0๐Ÿงช Negative Control)", "biological_system": "Deliberate 0๐Ÿงช Extreme AT-Rich (19.1% GC) Compositional Negative Control (Zero G4 / Zero Z-DNA)", "length_bp": 1500, "gc_percent": 2.8667, "cpg_obs_exp": 0.0, "cpg_island_count": 0, "native_g4_window_hits": 0, "ext_g4_window_hits": 0, "native_g4_merged_loci": 0, "ext_g4_merged_loci": 0, "g4_locus_sensitivity_pct": 100.0, "g4_locus_jaccard_iou": 1.0, "native_max_abs_g4_score": 0.04, "ext_max_abs_g4_score": 0.0, "mean_abs_delta_g4_score": 0.0, "native_zdna_hotspots": 0, "ext_zdna_hotspots": 0, "zdna_hotspot_jaccard_iou": 1.0, "native_min_delta_lk": 32.6886, "ext_min_delta_lk": 32.689, "mean_abs_delta_lk": 0.0, "native_max_z_score": 0.1323, "ext_max_z_score": 0.1323, "log10_zscore_pearson_r": 1.0, "peak_zdna_pos_1based": 5, "peak_zdna_motif": "ATAAATATTTAT", "peak_zdna_antisyn": "SASASASASASA", "top_g4_loci": [], "top_zdna_loci": [] } ], "ascii_master_summary_table": "========================================================================================================================================================\n NATIVE 4-STAGE NON-B DNA ENGINE vs. REFERENCE G4HUNTER (Bedrat et al. 2016) & Z-HUNT-II (zhunt3, Ho et al. 1986 / Schroth et al. 1992)\n========================================================================================================================================================\n Target Locus Accession Len(bp) GC% G4 Loci(Nat/Ext) Max|G4| G4 IoU Z-Hotspots(Nat/Ext) Min dLk(Nat/Ext) Max Z-Score\n--------------------------------------------------------------------------------------------------------------------------------------------------------\n pBR322_Ho1986_Vector J01749.1 4361 53.7% 5 / 5 1.56 1.0000 9 / 9 20.551 / 20.551 2.44e3\n Human_mtDNA_rCRS_Dloop_RNR NC_012920.1:1..4000 4000 45.0% 16 / 16 2.76 1.0000 10 / 10 20.049 / 20.049 4.83e3\n Ecoli_K12_rrnB_rpoB_Operon NC_000913.3:4166659..4168458 1800 52.2% 8 / 8 2.32 1.0000 32 / 32 17.031 / 17.031 5.76e5\n Streptomyces_SCO5087_actI_PKS NC_003888.3:5529801..5531600 1800 82.7% 12 / 12 2.72 1.0000 112 / 112 14.636 / 14.636 5.94e7\n Human_MYC_NHEIII1_ZDNA_Promoter NC_000008.11:127735000..127736599 1600 62.3% 11 / 11 2.72 1.0000 6 / 6 14.728 / 14.728 4.91e7\n Human_TOMM40_APOE_Exon4_CpG NC_000019.10:44905754..44907553 1800 74.2% 6 / 6 2.52 1.0000 58 / 58 14.217 / 14.217 1.44e8\n Human_chr1p36_Telomere_AGRN NC_000001.11:10001..11600 1600 72.2% 7 / 7 2.52 1.0000 96 / 96 16.799 / 16.799 8.74e5\n Pfalciparum_3D7_AT_Rich_Control NC_004331.3:221323..222822 1500 2.9% 0 / 0 0.04 1.0000 0 / 0 32.689 / 32.689 1.32e-1\n========================================================================================================================================================\n", "ascii_focal_myc_pbr322_alignment": "========================================================================================================================\n FOCAL STRUCTURAL ALIGNMENT A: HUMAN c-MYC PROMOTER NHE III_1 (PU27) PARALLEL G-QUADRUPLEX (NC_000008.11)\n========================================================================================================================\n Coord (nt) 1 10 20 27\n | | | |\n PU27 Sequence T GGGG A GGG T GGGG A GGG T GGGG AAGG\n G-Tetrad Core . [G1] . [G2]. [G3] . [G4]. [G5] .... (5 G-tracts enabling 1:2:1 loop isomerism)\n G4Hunter s_i 0 +444 0 +33 0 +444 0 +33 0 +444 0022 (Run-length quantized per-base G-skew)\n native_rust Window G4Hunter = +2.520 | Merged Locus = +2.52 | Parallel Intramolecular G4 (Tm = 84.5 C)\n G4Hunter_ref Window G4Hunter = +2.520 | Merged Locus = +2.52 | 100.0% Base-Score & Boundary Concordance\n Entropy Track โ– โ–ˆโ–ˆโ–ˆโ–ˆ โ– โ–ˆโ–ˆโ–ˆ โ– โ–ˆโ–ˆโ–ˆโ–ˆ โ– โ–ˆโ–ˆโ–ˆ โ– โ–ˆโ–ˆโ–ˆโ–ˆ โ–โ–โ–ƒโ–ƒ\n------------------------------------------------------------------------------------------------------------------------\n FOCAL STRUCTURAL ALIGNMENT B: CLONING VECTOR pBR322 CANONICAL B-TO-Z SUPERCOILING HOTSPOT (J01749.1:1446..1459)\n------------------------------------------------------------------------------------------------------------------------\n Coord (pBR322) 1446 1459\n | |\n pBR322 DNA C A C G G G T G C G C A T G (7 dinucleotides = 14 bp alternating Y-R core with GpG defect)\n Dinuc Steps CA CG GG TG CG CA TG\n Glycosidic A S A S A S A S A S A S A S (100% alternating anti-syn conformation without Z-Z junction)\n dG_B->Z (kcal) 1.4 0.7 2.4 1.4 0.7 1.4 1.4 (Sum dG_syn/anti = 9.32 kcal/mol + 2*5.0 kcal/mol B-Z junctions)\n native_rust Delta Lk_1/2 = 21.370 | Slope = 38.685 deg | Z-Score = 8.654e+02 (ASASASASASASAS)\n zhunt3_ref Delta Lk_1/2 = 21.370 | Slope = 38.685 deg | Z-Score = 8.654e+02 (ASASASASASASAS)\n========================================================================================================================\n", "total_duration_ms": 1738 }