Due to vast sequence divergence among different viral groups, sequence alignment is not directly applicable to genome-wide comparative analysis of viruses. More and more attention has been paid to alignment-free methods for whole genome comparison and phylogenetic tree reconstruction. Among alignment-free methods, the recently proposed ‘‘Natural Vector (NV) representation” has successfully been used to study the phylogeny of multi-segmented viruses based on a 12-dimensional genome space derived from the nucleotide sequence structure. But the preference of proteomes over genomes for the determination of viral phylogeny was not deeply investigated. As the translated products of genes, proteins directly form the shape of viral structure and are vital for all metabolic pathways. In this study, using the NV representation of a protein sequence along with the Hausdorff distance suitable to compare point sets, we construct a 60-dimensional protein space to analyze the evolutionary relationships of 4021 viruses by whole-proteomes in the current NCBI Reference Sequence Database (RefSeq). We also take advantage of the previously developed natural graphical representation to recover viral phylogeny. Our results demonstrate that the proposed method is efficient and accurate for classifying viruses. The accuracy rates of our predictions such as for Baltimore II viruses are as high as 95.9% for family labels, 95.7% for subfamily labels and 96.5% for genus labels. Finally, we discover that proteomes lead to better viral classification when reliable protein sequences are abundant. In other cases, the accuracy rates using proteomes are still comparable to that of genomes.

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The n-dimensional pair of pants is defined to be the complement of n + 2 generic hyperplanes in CPn. We construct an immersed Lagrangian sphere in the pair of pants and compute its endomorphism A1 algebra in the Fukaya category. On the level of cohomology, it is an exterior algebra with n+2 generators. It is not formal, and we compute certain higher products in order to determine it up to quasi-isomorphism. This allows us to give some evidence for the Homological Mirror Symmetry conjecture: the pair of pants is conjectured to be mirror to the Landau-Ginzburg model (Cn+2,W), where W = z1...zn+2. We show that the endomorphism A1 algebra of our Lagrangian is quasi-isomorphic to the endomorphism dg algebra of the structure sheaf of the origin in the mirror. This implies similar results for finite covers of the pair of pants, in particular for certain affine Fermat hypersurfaces.

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For periodic initial data with density allowed to vanish initially, we establish the global existence of strong and weak solutions to the two-dimensional barotropic compressible Navier–Stokes equations with no restrictions on the size of initial data provided the shear viscosity is a positive constant and the bulk one is λ =ρ^β with β>4/3. These results generalize and improve the previous ones due to Vaigant–Kazhikhov [Sib. Math. J. 36 (1995) 1283–1316] who required β>3. Moreover, we also prove that the densities for both the strong and weak solutions remain bounded from above independently of time. As a consequence, it is shown that both the strong and weak solutions converge to the equilibrium state as time tends to infinity.