Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. Results We first used simulated reads to explore the relationship between the level of compression and the error rate, the length of the reads and the level of sampling of the underlying genome and compare choices of second-stage compression algorithm. We demonstrate that compression may be greatly improved by a particular reordering of the sequences in the collection and give a novel `implicit sorting' strategy that enables these benefits to be realised without the overhead of sorting the reads. With these techniques, a 45x coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3Gbp of sequence to fit into only 8.2Gbytes of space (trimming a small proportion of low-quality bases from the reads improves the compression still further). This is more than 4 times smaller than the size achieved by a standard BWT-based compressor (bzip2) on the untrimmed reads, but an important further advantage of our approach is that it facilitates the building of compressed full text indexes such as the FM-index on large-scale DNA sequence collections.Comment: Version here is as submitted to Bioinformatics and is same as the previously archived version. This submission registers the fact that the advanced access version is now available at http://bioinformatics.oxfordjournals.org/content/early/2012/05/02/bioinformatics.bts173.abstract . Bioinformatics should be considered as the original place of publication of this article, please cite accordingl

A Rapid Cloning Method Employing Orthogonal End Protection

We describe a novel in vitro cloning strategy that combines standard tools in molecular biology with a basic protecting group concept to create a versatile framework for the rapid and seamless assembly of modular DNA building blocks into functional open reading frames. Analogous to chemical synthesis strategies, our assembly design yields idempotent composite synthons amenable to iterative and recursive split-and-pool reaction cycles. As an example, we illustrate the simplicity, versatility and efficiency of the approach by constructing an open reading frame composed of tandem arrays of a human fibronectin type III (FNIII) domain and the von Willebrand Factor A2 domain (VWFA2), as well as chimeric (FNIII)n-VWFA2-(FNIII)n constructs. Although we primarily designed this strategy to accelerate assembly of repetitive constructs for single-molecule force spectroscopy, we anticipate that this approach is equally applicable to the reconstitution and modification of complex modular sequences including structural and functional analysis of multi-domain proteins, synthetic biology or the modular construction of episomal vectors

Dynamics of PDMS- g-PDMS Bottlebrush Polymers by Broadband Dielectric Spectroscopy

Copyright © 2020 American Chemical Society. Poly(dimethylsiloxane) (PDMS)-based bottlebrush polymers, PDMS-g-PDMS, have been synthesized by anionic polymerization in combination with a condensation-based grafting reaction. Bottlebrush polymers show intriguing features, e.g., extremely low viscosities. Hereby, studies of their dynamics are rare. Therefore, we focus on the segmental relaxation by broadband dielectric spectroscopy. An increasing cross-sectional radius proportional to the increasing side chain length has been observed by small-angle neutron scattering over three samples. A comparison of the segmental relaxation times of the bottlebrushes with the respective linear chains reveals slower dynamics in the former. For longer chains, this effect vanishes

Towards Communication-Efficient Quantum Oblivious Key Distribution

Oblivious Transfer, a fundamental problem in the field of secure multi-party computation is defined as follows: A database DB of N bits held by Bob is queried by a user Alice who is interested in the bit DB_b in such a way that (1) Alice learns DB_b and only DB_b and (2) Bob does not learn anything about Alice's choice b. While solutions to this problem in the classical domain rely largely on unproven computational complexity theoretic assumptions, it is also known that perfect solutions that guarantee both database and user privacy are impossible in the quantum domain. Jakobi et al. [Phys. Rev. A, 83(2), 022301, Feb 2011] proposed a protocol for Oblivious Transfer using well known QKD techniques to establish an Oblivious Key to solve this problem. Their solution provided a good degree of database and user privacy (using physical principles like impossibility of perfectly distinguishing non-orthogonal quantum states and the impossibility of superluminal communication) while being loss-resistant and implementable with commercial QKD devices (due to the use of SARG04). However, their Quantum Oblivious Key Distribution (QOKD) protocol requires a communication complexity of O(N log N). Since modern databases can be extremely large, it is important to reduce this communication as much as possible. In this paper, we first suggest a modification of their protocol wherein the number of qubits that need to be exchanged is reduced to O(N). A subsequent generalization reduces the quantum communication complexity even further in such a way that only a few hundred qubits are needed to be transferred even for very large databases.Comment: 7 page

Weak and strong electronic correlations in Fe superconductors

In this chapter the strength of electronic correlations in the normal phase of Fe-superconductors is discussed. It will be shown that the agreement between a wealth of experiments and DFT+DMFT or similar approaches supports a scenario in which strongly-correlated and weakly-correlated electrons coexist in the conduction bands of these materials. I will then reverse-engineer the realistic calculations and justify this scenario in terms of simpler behaviors easily interpreted through model results. All pieces come together to show that Hund's coupling, besides being responsible for the electronic correlations even in absence of a strong Coulomb repulsion is also the origin of a subtle emergent behavior: orbital decoupling. Indeed Hund's exchange decouples the charge excitations in the different Iron orbitals involved in the conduction bands thus causing an independent tuning of the degree of electronic correlation in each one of them. The latter becomes sensitive almost only to the offset of the orbital population from half-filling, where a Mott insulating state is invariably realized at these interaction strengths. Depending on the difference in orbital population a different 'Mottness' affects each orbital, and thus reflects in the conduction bands and in the Fermi surfaces depending on the orbital content.Comment: Book Chapte

Measuring the defect structure orientation of a single NV- centre in diamond

The negatively charged nitrogen-vacancy (NV-) centre in diamond has many exciting applications in quantum nano-metrology, including magnetometry, electrometry, thermometry and piezometry. Indeed, it is possible for a single NV- centre to measure the complete three-dimensional vector of the local electric field or the position of a single fundamental charge in ambient conditions. However, in order to achieve such vector measurements, near complete knowledge of the orientation of the centres defect structure is required. Here, we demonstrate an optically detected magnetic resonance (ODMR) technique employing rotations of static electric and magnetic fields that precisely determines the orientation of the centres major and minor trigonal symmetry axes. Thus, our technique is an enabler of the centres existing vector sensing applications and also motivates new applications in multi-axis rotation sensing, NV growth characterization and diamond crystallography

TRUNCATULIX – a data warehouse for the legume community

Henckel K, Runte KJ, Bekel T, et al. TRUNCATULIX - a data warehouse for the legume community. BMC Plant Biology. 2009;9(1):19

TRUNCATULIX – a data warehouse for the legume community

Henckel K, Runte KJ, Bekel T, et al. TRUNCATULIX - a data warehouse for the legume community. BMC Plant Biology. 2009;9(1):19