Hawkeye: An interactive visual analytics tool for genome assemblies

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye. © 2007 Schatz et al.; licensee BioMed Central Ltd

pavarotti encodes a kinesin-like protein required to organize the central spindle and contractile ring for cytokinesis

Mutations in the Drosophila gene pavarotti result in the formation of abnormally large cells in the embryonic nervous system. In mitotic cycle 16, cells of pav mutant embryos undergo normal anaphase but then develop an abnormal telophase spindle and fail to undertake cytokinesis. We show that the septin Peanut, actin, and the actin-associated protein Anillin, do not become correctly localized in pav mutants. pav encodes a kinesin-like protein, PAV–KLP, related to the mammalian MKLP-1. In cellularized embryos, the protein is localized to centrosomes early in mitosis, and to the midbody region of the spindle in late anaphase and telophase. We show that Polo kinase associates with PAV–KLP with which it shows an overlapping pattern of subcellular localization during the mitotic cycle and this distribution is disrupted in pavmutants. We suggest that PAV–KLP is required both to establish the structure of the telophase spindle to provide a framework for the assembly of the contractile ring, and to mobilize mitotic regulator proteins

pavarotti encodes a kinesin-like protein required to organize the central spindle and contractile ring for cytokinesis

Mutations in the Drosophila gene pavarotti result in the formation of abnormally large cells in the embryonic nervous system. In mitotic cycle 16, cells of pav mutant embryos undergo normal anaphase but then develop an abnormal telophase spindle and fail to undertake cytokinesis. We show that the septin Peanut, actin, and the actin-associated protein Anillin, do not become correctly localized in pav mutants. pav encodes a kinesin-like protein, PAV–KLP, related to the mammalian MKLP-1. In cellularized embryos, the protein is localized to centrosomes early in mitosis, and to the midbody region of the spindle in late anaphase and telophase. We show that Polo kinase associates with PAV–KLP with which it shows an overlapping pattern of subcellular localization during the mitotic cycle and this distribution is disrupted in pavmutants. We suggest that PAV–KLP is required both to establish the structure of the telophase spindle to provide a framework for the assembly of the contractile ring, and to mobilize mitotic regulator proteins

Re-Assembly of the Genome of Francisella tularensis Subsp. holarctica OSU18

Francisella tularensis is a highly infectious human intracellular pathogen that is the causative agent of tularemia. It occurs in several major subtypes, including the live vaccine strain holarctica (type B). F. tularensis is classified as category A biodefense agent in part because a relatively small number of organisms can cause severe illness. Three complete genomes of subspecies holarctica have been sequenced and deposited in public archives, of which OSU18 was the first and the only strain for which a scientific publication has appeared [1]. We re-assembled the OSU18 strain using both de novo and comparative assembly techniques, and found that the published sequence has two large inversion mis-assemblies. We generated a corrected assembly of the entire genome along with detailed information on the placement of individual reads within the assembly. This assembly will provide a more accurate basis for future comparative studies of this pathogen

Surface correlations for two-dimensional Coulomb fluids in a disc

After a brief review of previous work, two exactly solvable two-dimensional models of a finite Coulomb fluid in a disc are studied. The charge correlation function near the boundary circle is computed. When the disc radius is large compared to the bulk correlation length, a correlation function of the surface charge density can be defined. It is checked, on the solvable models, that this correlation function does have the generic long-range behaviour, decaying as the inverse square distance, predicted by macroscopic electrostatics. In the case of a two-component plasma (Coulomb fluid made of two species of particles of opposite charges), the density correlation function on the boundary circle itself is conjectured to have a temperature-independent behaviour, decaying as the -4 power of the distance.Comment: 15 pages, Latex, submitted to J.Phys.:Condens.Matte

Equation of state in the fugacity format for the two-dimensional Coulomb gas

We derive the exact general form of the equation of state, in the fugacity format, for the two-dimensional Coulomb gas. Our results are valid in the conducting phase of the Coulomb gas, for temperatures above the Kosterlitz-Thouless transition. The derivation of the equation of state is based on the knowledge of the general form of the short-distance expansion of the correlation functions of the Coulomb gas. We explicitly compute the expansion up to order $O(\zeta^6)$ in the activity $\zeta$. Our results are in very good agreement with Monte Carlo simulations at very low density

Long-range interactions and non-extensivity in ferromagnetic spin models

The Ising model with ferromagnetic interactions that decay as $1/r^\alpha$ is analyzed in the non-extensive regime $0\leq\alpha\leq d$, where the thermodynamic limit is not defined. In order to study the asymptotic properties of the model in the $N\rightarrow\infty$ limit ($N$ being the number of spins) we propose a generalization of the Curie-Weiss model, for which the $N\rightarrow\infty$ limit is well defined for all $\alpha\geq 0$. We conjecture that mean field theory is {\it exact} in the last model for all $0\leq\alpha\leq d$. This conjecture is supported by Monte Carlo heat bath simulations in the $d=1$ case. Moreover, we confirm a recently conjectured scaling (Tsallis\cite{Tsallis}) which allows for a unification of extensive ($\alpha>d$) and non-extensive ($0\leq\alpha\leq d$) regimes.Comment: RevTex, 12 pages, 1 eps figur

Data Mining and Machine Learning in Astronomy

We review the current state of data mining and machine learning in astronomy. 'Data Mining' can have a somewhat mixed connotation from the point of view of a researcher in this field. If used correctly, it can be a powerful approach, holding the potential to fully exploit the exponentially increasing amount of available data, promising great scientific advance. However, if misused, it can be little more than the black-box application of complex computing algorithms that may give little physical insight, and provide questionable results. Here, we give an overview of the entire data mining process, from data collection through to the interpretation of results. We cover common machine learning algorithms, such as artificial neural networks and support vector machines, applications from a broad range of astronomy, emphasizing those where data mining techniques directly resulted in improved science, and important current and future directions, including probability density functions, parallel algorithms, petascale computing, and the time domain. We conclude that, so long as one carefully selects an appropriate algorithm, and is guided by the astronomical problem at hand, data mining can be very much the powerful tool, and not the questionable black box.Comment: Published in IJMPD. 61 pages, uses ws-ijmpd.cls. Several extra figures, some minor additions to the tex