Compressing DNA sequence databases with coil

Background: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion: coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci collected across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g., exons). However, molecular techniques requiring RNA as a template are limited to using very high quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n$=$1510) of ultraconserved elements (UCE) shared among the insect order Hymenoptera. We use in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled Hymenoptera, and we design a set of baits for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We use our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic relationships spanning very old ($\geq$220 MYA) to very young ($\leq$1 MYA) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support

France and the Bretton Woods International Monetary System: 1960-1968

We reinterpret the commonly held view in the U.S. that France, by following a policy from 1965 to 1968 of deliberately converting their dollar holdings into gold helped perpetuate the collapse of the Bretton Woods International Monetary System. We argue that French international monetary policy under Charles de Gaulle was consistent with strategies developed in the interwar period and the French Plan of 1943. France used proposals to return to an orthodox gold standard as well as conversions of its dollar reserves into gold as tactical threats to induce the United States to initiate the reform of the international monetary system towards a more symmetrical and cooperative gold-exchange standard regime.

Chandra Observation of the Radio Source / X-ray Gas Interaction in the Cooling Flow Cluster Abell 2052

We present a Chandra observation of Abell 2052, a cooling flow cluster with a central cD that hosts the complex radio source 3C 317. The data reveal ``holes'' in the X-ray emission that are coincident with the radio lobes. The holes are surrounded by bright ``shells'' of X-ray emission. The data are consistent with the radio source displacing and compressing, and at the same time being confined by, the X-ray gas. The compression of the X-ray shells appears to have been relatively gentle and, at most, slightly transonic. The pressure in the X-ray gas (the shells and surrounding cooler gas) is approximately an order of magnitude higher than the minimum pressure derived for the radio source, suggesting that an additional source of pressure is needed to support the radio plasma. The compression of the X-ray shells has speeded up the cooling of the shells, and optical emission line filaments are found coincident with the brightest regions of the shells.Comment: accepted for publication in ApJ Letters; for high-resolution color figures, see http://www.astro.virginia.edu/~elb6n/abell2052.htm

The Gravitational Lens Candidate FBQ 1633+3134

We present our ground-based optical imaging, spectral analysis, and high resolution radio mapping of the gravitational lens candidate FBQ 1633+3134. This z=1.52, B=17.7 quasar appears double on CCD images with an image separation of 0.66 arcseconds and a flux ratio of ~3:1 across BVRI filters. A single 0.27 mJy radio source is detected at 8.46 GHz, coincident to within an arcsecond of both optical components, but no companion at radio wavelengths is detected down to a flux level of 0.1 mJy (3 sigma). Spectral observations reveal a rich metal-line absorption system consisting of a strong Mg II doublet and associated Fe I and Fe II absorption features, all at an intervening redshift of z=0.684, suggestive of a lensing galaxy. Point spread function subtraction however shows no obvious signs of a third object between the two quasar images, and places a detection limit of I > 23.0 if such an object exists. Although the possibility that FBQ 1633+3134 is a binary quasar cannot be ruled out, the evidence is consistent with it being a single quasar lensed by a faint, metal-rich galaxy.Comment: 24 pages, 5 figures. Accepted by AJ. A calibration error affecting B and V band apparent magnitudes has been corrected. The conclusions of the paper are not change

A global fit of top quark effective theory to data

In this paper we present a global fit of beyond the Standard Model (BSM) dimension six operators relevant to the top quark sector to currently available data. Experimental measurements include parton-level top-pair and single top production from the LHC and the Tevatron. Higher order QCD corrections are modelled using differential and global K-factors, and we use novel fast-fitting techniques developed in the context of Monte Carlo event generator tuning to perform the fit. This allows us to provide new, fully correlated and model-independent bounds on new physics effects in the top sector from the most current direct hadron-collider measurements in light of the involved theoretical and experimental systematics. As a by-product, our analysis constitutes a proof-of-principle that fast fitting of theory to data is possible in the top quark sector, and paves the way for a more detailed analysis including top quark decays, detector corrections and precision observables.Comment: Additional references and preprint code added. Minor error in generation of plots fixed, no conclusions affecte

An FeLoBAL Binary Quasar

In an ongoing infrared imaging survey of quasars at Keck Observatory, we have discovered that the z=1.285 quasar SDSS J233646.2-010732.6 comprises two point sources with a separation of 1.67". Resolved spectra show that one component is a standard quasar with a blue continuum and broad emission lines; the other is a broad absorption line (BAL) quasar, specifically, a BAL QSO with prominent absorption from MgII and metastable FeII, making it a member of the ``FeLoBAL'' class. The number of known FeLoBALs has recently grown dramatically from a single example to more than a dozen, including a gravitationally lensed example and the binary member presented here, suggesting that this formerly rare object may be fairly common. Additionally, the presence of this BAL quasar in a relatively small separation binary adds to the growing evidence that the BAL phenomenon is not due to viewing a normal quasar at a specific orientation, but rather that it is an evolutionary phase in the life of many, if not all, quasars, and is particularly associated with conditions found in interacting systems.Comment: AASTEX 13 pp., 4 figs; accepted by ApJ Letter

Foreground Predictions for the Cosmic Microwave Background Power Spectrum from Measurements of Faint Inverted Radio Sources at 5 GHz

We present measurements of a population of matched radio sources at 1.4 and 5 GHz down to a flux limit of 1.5 mJy in 7 sq. degs. of the NOAO Deep Field South. We find a significant fraction of sources with inverted spectral indices that all have 1.4 GHz fluxes less than 10 mJy, and are therefore too faint to have been detected and included in previous radio source count models that are matched at multiple frequencies. Combined with the matched source population at 1.4 and 5 GHz in 1 sq. deg. in the ATESP survey, we update models for the 5 GHz differential number counts and distributions of spectral indices in 5 GHz flux bins that can be used to estimate the unresolved point source contribution to the cosmic microwave background temperature anisotropies. We find a shallower logarithmic slope in the 5 GHz differential counts than in previously published models for fluxes < 100 mJy as well as larger fractions of inverted spectral indices at these fluxes. Because the Planck flux limit for resolved sources is larger than 100 mJy in all channels, our modified number counts yield at most a 10% change in the predicted Poisson contribution to the Planck temperature power spectrum. For a flux cut of 5 mJy with the South Pole Telescope and a flux cut of 20 mJy with the Atacama Cosmology Telescope we predict a ~30% and ~10% increase, respectively, in the radio source Poisson power in the lowest frequency channels of each experiment relative to that predicted by previous models.Comment: 14 pages, 9 figures, includes ApJ proof correction