ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes

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: . 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

Quantum correlation and classical correlation dynamics in the spin-boson model

We study the quantum correlation and classical correlation dynamics in a spin-boson model. For two different forms of spectral density, we obtain analytical results and show that the evolutions of both correlations depend closely on the form of the initial state. At the end of evolution, all correlations initially stored in the spin system transfer to reservoirs. It is found that for a large family of initial states, quantum correlation remains equal to the classical correlation during the course of evolution. In addition, there is no increase in the correlations during the course of evolution.Comment: 10 pages, 5 figure

catena-Poly[[(2,2′-bipyridine)­nickel(II)]-μ-2,4′-oxydibenzoato]

In the title compound, [Ni(C14H8O5)(C10H8N2)]n, the NiII atom is six-coordinated in a slightly distorted octa­hedral geometry by four O atoms from two chelating carboxyl­ate groups of symmetry-related 2,4′-oxydibenzoate anions and by two N atoms from a 2,2′-bipyridine ligand. The NiII atoms are bridged by the 2,4′-oxydibenzoate anions, resulting in the formation of helical chains parallel to [010] with a repeating unit of 15.039 (2) Å