Relative Select

Motivated by the problem of storing coloured de Bruijn graphs, we show how, if we can already support fast select queries on one string, then we can store a little extra information and support fairly fast select queries on a similar string

Evolution of the pygmy dipole resonance in nuclei with neutron excess

The electric dipole excitation of various nuclei is calculated with a Random Phase Approximation phenomenological approach. The evolution of the strength distribution in various groups of isotopes, oxygen, calcium, zirconium and tin, is studied. The neutron excess produces $E1$ strength in the low energy region. Indexes to measure the collectivity of the excitation are defined. We studied the behavior of proton and neutron transition densities to determine the isoscalar or isovector nature of the excitation. We observed that in medium-heavy nuclei the low-energy $E1$ excitation has characteristics rather different that those exhibited by the giant dipole resonance. This new type of excitation can be identified as pygmy dipole resonance.Comment: 14 pages, 12 figures, 7 table

Evolution of the pygmy dipole resonance in nuclei with neutron excess

The electric dipole excitation of various nuclei is calculated with a Random Phase Approximation phenomenological approach. The evolution of the strength distribution in various groups of isotopes, oxygen, calcium, zirconium and tin, is studied. The neutron excess produces $E1$ strength in the low energy region. Indexes to measure the collectivity of the excitation are defined. We studied the behavior of proton and neutron transition densities to determine the isoscalar or isovector nature of the excitation. We observed that in medium-heavy nuclei the low-energy $E1$ excitation has characteristics rather different that those exhibited by the giant dipole resonance. This new type of excitation can be identified as pygmy dipole resonance.Comment: 14 pages, 12 figures, 7 table

Compressed Text Indexes:From Theory to Practice!

A compressed full-text self-index represents a text in a compressed form and still answers queries efficiently. This technology represents a breakthrough over the text indexing techniques of the previous decade, whose indexes required several times the size of the text. Although it is relatively new, this technology has matured up to a point where theoretical research is giving way to practical developments. Nonetheless this requires significant programming skills, a deep engineering effort, and a strong algorithmic background to dig into the research results. To date only isolated implementations and focused comparisons of compressed indexes have been reported, and they missed a common API, which prevented their re-use or deployment within other applications. The goal of this paper is to fill this gap. First, we present the existing implementations of compressed indexes from a practitioner's point of view. Second, we introduce the Pizza&Chili site, which offers tuned implementations and a standardized API for the most successful compressed full-text self-indexes, together with effective testbeds and scripts for their automatic validation and test. Third, we show the results of our extensive experiments on these codes with the aim of demonstrating the practical relevance of this novel and exciting technology

Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared