Table 3.

A Partial List of Z-curve Applications in Genome Analysis.

Research areas	Involved Z-Curve Components	Algorithm, Software or Database	Life Domains or Virus	Species
Protein-coding gene recognition a	x, y, z, S	Z-curve algorithm [1, 2], Zcurve [12]	Bacteria	Acinetobacter baumannii [17], Variovorax paradoxus [18], Amycolatopsis mediterranei [19], Bacillus thuringiensis [20], Streptomyces tendae [21], Phaeobacter gallaeciensis [22], Desulfobacterium autotrophicum [23], Mycobacterium tuberculosis [24], Magnetospirillum gryphiswaldense [25], Beggiatoa [26]
			Phage, plasmid	Fosmids of marine Planctomycetes [127], plasmids in the human gut [128], phage Rtp [129]
			Archaea	Archaea of the ANME-1 group [27]
			Eukaryotes	Leptospira interrogans [130], Yeast [11], Short human protein-coding genes [56, 131], Drosophila [55]
		Zcurve_V [14], Zcurve_CoV [15]	Virus, Coronavirus, phages	Prophage [33], Me Tri virus [28], novel human coronaviruses NL63 and HKU1 [34], novel bat coronaviruses [35], bat coronaviruses 1A, 1B and HKU8 [36], novel human coronavirus [37]
			SARS_CoV	Various strains of SARS_CoV [38-53]
Replication origin identification	AT, GC, MK and RY disparity b	Ori-finder [78], DoriC [132, 133]	Archaea	Methanosarcina mazei[69], Halobacterium species NRC-1[63], Methanocaldococcus jannaschii [68], Sulfolobus acidocaldarius [72], Haloferax volcanii [73], Desulfurococcus kamchatkensis [74], Thermococcus sibiricus [75], Sulfolobus islandicus [76]
			Bacteria	Moraxella catarrhalis [79], Sorangium cellulosum [80],  Microcystis aeruginosa [80], Cyanothece [81], Cupriavidus metallidurans [82], Azolla filiculoides [83], Variovorax paradoxus [18], Corynebacterium pseudotuberculosis [84], [85], Orientia tsutsugamushi [86], Propionibacterium freudenreichii [87], Laribacter hongkongensis [88], Legionella pneumophila [89], Ehrlichia canis [90]
			Phage, plasmid	Streptococcus pneumoniae Virulent Phage Dp-1 [134], R-plasmid pPRS3a from Bacillus cereus [135]
Genomic island identification	z’	GC profile [9, 10]	Bacteria	Corynebacterium efficiens [105], Rhodopseudomonas palustris [106], Corynebacterium glutamicum [104], Vibrio vulnificus and Bacillus cereus [103], Agrobacterium tumefaciens, Rolstonia solanacearum, Xanthomonas axonopodis, Xanthomonas campestris, Xylella fastidiosa and Pseudomonas syringae [107], Streptomyces lividans [108], Parachlamydiaceae UWE25 [109], epsilon proteobacteria Sulfurovum and Nitratiruptor [110], Acinetobacter oleivorans [111], Silicibacter pomeroyi [112]
			Archaea	Haloquadratum walsbyi [136]
GC content variation,	z’, S	GC profile [9, 10]	Eukaryotes	Human genome: isochores [94, 98, 137] and replication time zones [138]; Isochores for chicken [97], Arabidopsis thaliana [96], mice [95] and pig [99]; DNA curvature profile for Aspergillus fumigatus [100]
isochore, genome segmentation			Bacteria	Bifidobacterium longum [139], Streptomyces avermitilis [140], Erwinia amylovora [141], Ralstonia pickettii [142]
Promoter, translational start sites, nucleosome positioning	x, y, z	Z-curve algorithm [11, 12], GS-finder [113]	Bacteria	Translational start sites [113] and promoters [115] of Escherichia coli and Bacillus subtilis
			Eukaryotes	Human Pol II promoter [114], Yeast genome for stable and dynamic nucleosome positioning [116]
Comparative genomics, genome visualization	x, y, z, z’	Z-curve database [117]	Bacteria, archaea, eukaryotes and viruses	Bacillus cereus [103], Bacillus cereus ATCC 10987 [119], Coronavirus [118], human immunodeficiency virus [120], human [121, 143], E. coli [122], Seven GC-rich bacteria [126], 90 species [1], Aeropyrum pernix K1 [124], Streptomyces coelicolor [125]