progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms.We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs breakpoint score, which facilitates accurate detection of rearrangement breakpoints when genomes have unequal gene content. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The new genome alignment algorithm demonstrates high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental gain and loss. We apply the new algorithm to a set of 23 genomes from the genera Escherichia, Shigella, and Salmonella. Analysis of whole-genome multiple alignments allows us to extend the previously defined concepts of core- and pan-genomes to include not only annotated genes, but also non-coding regions with potential regulatory roles. The 23 enterobacteria have an estimated core-genome of 2.46Mbp conserved among all taxa and a pan-genome of 15.2Mbp. We document substantial population-level variability among these organisms driven by segmental gain and loss. Interestingly, much variability lies in intergenic regions, suggesting that the Enterobacteriacae may exhibit regulatory divergence.The multiple genome alignments generated by our software provide a platform for comparative genomic and population genomic studies. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve

A complete quantum mechanical study of chlorine photodissociation.

A fully quantum mechanical dynamical calculation on the photodissociation of molecular chlorine is presented. The magnitudes and phases of all the relevant photofragment T-matrices have been calculated, making this study the computational equivalent of a "complete experiment," where all the possible parameters defining an experiment have been determined. The results are used to simulate cross-sections and angular momentum polarization information which may be compared with experimental data. The calculations rigorously confirm the currently accepted mechanism for the UV photodissociation of Cl(2), in which the majority of the products exit on the C(1)Π(1u) state, with non-adiabatic couplings to the A(3)Π(1u) and several other Ω = 1 states, and a small contribution from the B(3)Π state present at longer wavelengths

The vibrationally mediated photodissociation of Cl2.

The photodissociation of vibrationally excited Cl(2)(v = 1) has been investigated experimentally using the velocity mapped ion imaging technique. The experimental measurements presented here are compared with the results of time-dependent wavepacket calculations performed on a set of ab initio potential energy curves. The high level calculations allow prediction of all the dynamical information regarding the dissociation, including electronic polarization effects. Using a combination of theory and experiment it was found that there was negligible cooling of the vibrational degree of freedom of the parent molecule in the molecular beam. The results presented are compared with those following the photodissociation of Cl(2)(v = 0). Although the same electronic states are found to be important for Cl(2)(v = 1) as for Cl(2)(v = 0), significant differences were found regarding many of the observables. The overall level of agreement between theory and experiment was found to be reasonable and confirms previous assignments of the photodissociation mechanism

Electronic polarization effects in the photodissociation of Cl2.

Velocity mapped ion imaging and resonantly enhanced multiphoton ionization time-of-flight methods have been used to investigate the photodissociation dynamics of the diatomic molecule Cl(2) following excitation to the first UV absorption band. The experimental results presented here are compared with high level time dependent wavepacket calculations performed on a set of ab initio potential energy curves [D. B. Kokh, A. B. Alekseyev, and R. J. Buenker, J. Chem. Phys. 120, 11549 (2004)]. The theoretical calculations provide the first determination of all dynamical information regarding the dissociation of a system of this complexity, including angular momentum polarization. Both low rank K = 1, 2 and high rank K = 3 electronic polarization are predicted to be important for dissociation into both asymptotic product channels and, in general, good agreement is found between the recent theory and the measurements made here, which include the first experimental determination of high rank K = 3 orientation

Control of ultrafast molecular photodissociation by laser-field-induced potentials

Depto. de Química FísicaFac. de Ciencias QuímicasTRUEpu