CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis

Coronavirus Genomics and Bioinformatics Analysis

The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999–2002, with estimated substitution rate of 4×10−4 to 2×10−2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses

A special irreducible matrix representation of the real Clifford algebra C(3,1)

4x4 Dirac (gamma) matrices (irreducible matrix representations of the Clifford algebras C(3,1), C(1,3), C(4,0)) are an essential part of many calculations in quantum physics. Although the final physical results do not depend on the applied representation of the Dirac matrices (e.g. due to the invariance of traces of products of Dirac matrices), the appropriate choice of the representation used may facilitate the analysis. The present paper introduces a particularly symmetric real representation of 4x4 Dirac matrices (Majorana representation) which may prove useful in the future. As a byproduct, a compact formula for (transformed) Pauli matrices is found. The consideration is based on the role played by isoclinic 2-planes in the geometry of the real Clifford algebra C(3,0) which provide an invariant geometric frame for it. It can be generalized to larger Clifford algebras.Comment: 23 pages LaTeX, to appear in the J. Math. Phys. (v2: appendix B on Pauli matrices and references are added, minor other changes

Lightpath Affiliation Graph Approach for Wavelength Assignment of Lambda Leasing Service

Abstract In view of practical engineering and service deployment requirements, we propose to apply Lightpath Affiliation Graph partitioning heuristic for the wavelength assignment in mesh optical transport networks to support emerging lambda leasing service

Statistics of self-avoiding walks on randomly diluted lattice

A comprehensive numerical study of self-avoiding walks (SAW's) on randomly diluted lattices in two and three dimensions is carried out. The critical exponents $\nu$ and $\chi$ are calculated for various different occupation probabilities, disorder configuration ensembles, and walk weighting schemes. These results are analyzed and compared with those previously available. Various subtleties in the calculation and definition of these exponents are discussed. Precise numerical values are given for these exponents in most cases, and many new properties are recognized for them.Comment: 34 pages (+ 12 figures), REVTEX 3.

Effects of Impurities in Random Sequential Adsorption on a One-Dimensional Substrate

We have solved the kinetics of random sequential adsorption of linear $k$-mers on a one-dimensional disordered substrate for the random sequential adsorption initial condition and for the random initial condition. The jamming limits $\theta(\infty, k', k)$ at fixed length of linear $k$-mers have a minimum point at a particular density of the linear $k'$-mers impurity for both cases. The coverage of the surface and the jamming limits are compared to the results for Monte Carlo simulation. The Monte Carlo results for the jamming limits are in good agreement with the analytical results. The continuum limits are derived from the analytical results on lattice substrates.Comment: 9 pages, latex, 1 figure not included, accepted in Phys. Rev.

Half-Metallic Graphene Nanoribbons

Electrical current can be completely spin polarized in a class of materials known as half-metals, as a result of the coexistence of metallic nature for electrons with one spin orientation and insulating for electrons with the other. Such asymmetric electronic states for the different spins have been predicted for some ferromagnetic metals - for example, the Heusler compounds- and were first observed in a manganese perovskite. In view of the potential for use of this property in realizing spin-based electronics, substantial efforts have been made to search for half-metallic materials. However, organic materials have hardly been investigated in this context even though carbon-based nanostructures hold significant promise for future electronic device. Here we predict half-metallicity in nanometre-scale graphene ribbons by using first-principles calculations. We show that this phenomenon is realizable if in-plane homogeneous electric fields are applied across the zigzag-shaped edges of the graphene nanoribbons, and that their magnetic property can be controlled by the external electric fields. The results are not only of scientific interests in the interplay between electric fields and electronic spin degree of freedom in solids but may also open a new path to explore spintronics at nanometre scale, based on graphene