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

An Investigation of the Role of Exchange Rates on U.S. Exports of Selected Agricultural Products: 1968-1983

An· econometric partial equilibrium trade model of the U.S. corn, wheat, soybean, cotton, and tobacco market is developed for the yearly periods 1968-1983. The effect of real exchange rates, real price, and demand factors on the exports of each commodity is examined to test the hypothesis that monetary factors can affect the agricultural sector. An examination of the elasticities of real price, real exchange rate, and real income indicate that an extremely inelastic response to both price movements and exchange rate adjustments. Foreign buying power is the strongest explanatory variable. An exchange rate linkage with the agricultural sector is not proven.International Relations/Trade,

Understanding nominal GNP targeting

Gross national product

THE INDUSTRIALIZATION OF AGRICULTURE: IMPLICATIONS FOR FUTURE POLICY

Farming is in the midst of a major transformation—not only in technology and production practices, but also in size of business, resource (land) control and operation, business model and linkages with buyers and suppliers. This paper describes the fundamental drivers of today’s structural change in U.S. agriculture. The impact of the drivers are illustrated by describing some illustrations of the kinds of innovative farming operations that are developing in agriculture, not the typical farms but those who appear to be leading and shaping the new agriculture. Finally, farm policy implications of the transformation of farming to an industrial manufacturing model are discussed.Farm policy, industrialization of agriculture, structural change, biological manufacturing

Testing for a pure state with local operations and classical communication

We examine the problem of using local operations and classical communication (LOCC) to distinguish a known pure state from an unknown (possibly mixed) state, bounding the error probability from above and below. We study the asymptotic rate of detecting multiple copies of the pure state and show that, if the overlap of the two states is great enough, then they can be distinguished asymptotically as well with LOCC as with global measurements; otherwise, the maximal Schmidt coefficient of the pure state is sufficient to determine the asymptotic error rate.Comment: 11 pages, 2 figures. Published version with small revisions and expanded title

The telomerase essential N-terminal domain promotes DNA synthesis by stabilizing short RNA-DNA hybrids.

Telomerase is an enzyme that adds repetitive DNA sequences to the ends of chromosomes and consists of two main subunits: the telomerase reverse transcriptase (TERT) protein and an associated telomerase RNA (TER). The telomerase essential N-terminal (TEN) domain is a conserved region of TERT proposed to mediate DNA substrate interactions. Here, we have employed single molecule telomerase binding assays to investigate the function of the TEN domain. Our results reveal telomeric DNA substrates bound to telomerase exhibit a dynamic equilibrium between two states: a docked conformation and an alternative conformation. The relative stabilities of the docked and alternative states correlate with the number of basepairs that can be formed between the DNA substrate and the RNA template, with more basepairing favoring the docked state. The docked state is further buttressed by the TEN domain and mutations within the TEN domain substantially alter the DNA substrate structural equilibrium. We propose a model in which the TEN domain stabilizes short RNA-DNA duplexes in the active site of the enzyme, promoting the docked state to augment telomerase processivity

Perturbed angular correlation study of a haptenic molecule

The angular correlation of the 173-247 keV gamma-ray cascade after the electron-capture decay of (111)In is strongly perturbed when the I-p-nitrophenylethylenediaminetetraacetate chelate of (111)In(3+) is added to a solution containing rabbit antibody to dinitrophenyl groups. The radioactive chelate can be displaced by the addition of dinitrophenyllysine or unlabeled chelate. The average association constant between the antibody and the labeled chelate has been estimated from perturbed angular correlation measurements; this value is compared to the results of equilibrium dialysis. These experiments provide good evidence that information concerning macromolecular behavior can be obtained from perturbed angular correlation experiments that use chemically specific labels