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C20H40Cl2CuKO10, triclinic, P1‾$P\overline{1}$ (no. 2), a = 9.0148(5) Å, b = 9.3066(5) Å, c = 17.7296(10) Å, α = 78.383(2)°$78.383(2){}^{\circ}$, β = 88.488(2)°$88.488(2){}^{\circ}$, γ = 72.982(2)°$72.982(2){}^{\circ}$, V = 1392.35(13) Å3, Z = 2, Rgt(F) = 0.0781, wRref(F2) = 0.2089, T = 170(2) K.

Abstract Background Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins (oriCs) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of genome sequencing, the current available software for predicting oriCs, however, still leaves much to be desired. Therefore, the increasing availability of genome sequences calls for improved software to identify oriCs in newly sequenced and unannotated bacterial genomes. Results We have developed Ori-Finder, an online system for finding oriCs in bacterial genomes based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve method, distribution of DnaA boxes, and the occurrence of genes frequently close to oriCs. The program can also deal with unannotated genome sequences by integrating the gene-finding program ZCURVE 1.02. Output of the predicted results is exported to an HTML report, which offers convenient views on the results in both graphical and tabular formats. Conclusion A web-based system to predict replication origins of bacterial genomes has been presented here. Based on this system, oriC regions have been predicted for the bacterial genomes available in GenBank currently. It is hoped that Ori-Finder will become a useful tool for the identification and analysis of oriCs in both bacterial and archaeal genomes.

Abstract Background It necessary to use highly accurate and statistics-based systems for viral and phage genome annotations. The GeneMark systems for gene-finding in virus and phage genomes suffer from some basic drawbacks. This paper puts forward an alternative approach for viral and phage gene-finding to improve the quality of annotations, particularly for newly sequenced genomes. Results The new system ZCURVE_V has been run for 979 viral and 212 phage genomes, respectively, and satisfactory results are obtained. To have a fair comparison with the currently available software of similar function, GeneMark, a total of 30 viral genomes that have not been annotated by GeneMark are selected to be tested. Consequently, the average specificity of both systems is well matched, however the average sensitivity of ZCURVE_V for smaller viral genomes (< 100 kb), which constitute the main parts of viral genomes sequenced so far, is higher than that of GeneMark. Additionally, for the genome of Amsacta moorei entomopoxvirus, probably with the lowest genomic GC content among the sequenced organisms, the accuracy of ZCURVE_V is much better than that of GeneMark, because the later predicts hundreds of false-positive genes. ZCURVE_V is also used to analyze well-studied genomes, such as HIV-1, HBV and SARS-CoV. Accordingly, the performance of ZCURVE_V is generally better than that of GeneMark. Finally, ZCURVE_V may be downloaded and run locally, particularly facilitating its utilization, whereas GeneMark is not downloadable. Based on the above comparison, it is suggested that ZCURVE_V may serve as a preferred gene-finding tool for viral and phage genomes newly sequenced. However, it is also shown that the joint application of both systems, ZCURVE_V and GeneMark, leads to better gene-finding results. The system ZCURVE_V is freely available at: http://tubic.tju.edu.cn/Zcurve_V/. Conclusion ZCURVE_V may serve as a preferred gene-finding tool used for viral and phage genomes, especially for anonymous viral and phage genomes newly sequenced.

C20H40Cl2CuKO10, triclinic, P 1 ‾ (no. 2), a = 9.0148(5) Å, b = 9.3066(5) Å, c = 17.7296(10) Å, α = 78.383 (2) ° , β = 88.488 (2) ° , γ = 72.982 (2) ° , V = 1392.35(13) Å3, Z = 2, Rgt(F) = 0.0781, wRref(F2) = 0.2089, T = 170(2) K. [ABSTRACT FROM AUTHOR]

C20H40Cl2CuKO10, triclinic, P 1 ‾ (no. 2), a = 9.0148(5) Å, b = 9.3066(5) Å, c = 17.7296(10) Å, α = 78.383 (2) ° , β = 88.488 (2) ° , γ = 72.982 (2) ° , V = 1392.35(13) Å3, Z = 2, Rgt(F) = 0.0781, wRref(F2) = 0.2089, T = 170(2) K. [ABSTRACT FROM AUTHOR]