Search results for "algorithm."

Change-point estimation in piecewise constant regression models with random effects

2014

We propose an iterative algorithm to estimate change-points in general regression models. The algorithm avoids grid search to obtain maximum likelihood estimates, and thus it guarantees moderate computational time regardless of the sample size and the number of change-points to be estimated. Furthermore, it allows estimation in random effects models, where grid search is unfeasible. We present the proposed approach in practice by analyzing variations of lung functionality on a sample of transplant recipients.

Prediction of the retention in reversed-phase liquid chromatography using solute-mobile phase-stationary phase polarity parameters.

2002

Abstract A previously reported algorithm, based on the equation: log k=( log k) 0 +p(P N m −P N s ) , that relates the retention in reversed-phase liquid chromatography with solute (p), mobile phase (PmN) and stationary phase (PsN) relative polarity parameters, is improved. The retention data reported by several authors for different sets of compounds, eluted with acetonitrile–water and methanol–water mixtures, are used to test the algorithm and elaborate a database of p values. The methodology is successfully applied to predict the retention using PmN values calculated as PmN=1.00−(2.13ϕ)/(1+1.42ϕ) for acetonitrile–water and PmN=1.00−(1.33ϕ)/(1+0.47ϕ) for methanol–water, ϕ being the organi…

A Solution to the Problem of the Maximal Number of Symbols for Biomolecular Computer

2019

The authors present a solution to the problem of generating the maximum possible number of symbols for a biomolecular computer using restriction enzyme BbvI and ligase as the hardware, and transition molecules built of double-stranded DNA as the software. The presented solution offers an answer to the open question, in the algorithm form, of the maximal number of symbols for a biomolecular computer that makes use of the restriction enzyme BbvI.

Affinity Distributions of a Molecularly Imprinted Polymer Calculated Numerically by the Expectation-Maximization Method

2003

Affinity distributions are calculated from adsorption isotherm data obtained for the enantiomers of L- and D-phenylalanine anilide (PA) on native and thermally annealed polymers molecularly imprinted with L-PA. The calculation is obtained with an iterative algorithm called expectation-maximization that does not require prior fit of the data to an isotherm model before inversion and thus yields a distribution indicative of the data only. The results show bimodal distributions, suggestive of a two-site model describing relatively selective and nonselective adsorption modes of the L-enantiomer and a corresponding unimodal/nonselective adsorption mode for the D-enantiomer. The nonselective adso…

Competition between liquid-crystalline ordering and glassy freezing in melts of semiflexible polymers: A monte carlo simulation

1999

We present results of a Monte Carlo simulation of dense melts of semiflexible polymers using the bond-fluctuation model. The chosen Hamiltonian increases the chain stiffness upon cooling which in turn leads to glass-transition like freezing of the polymer mobility. Employing an efficient simulation algorithm, which is able to equilibrate the simulated systems to lower temperature than the Rouse-type algorithm showing the glassy freezing, we are able to observe an isotropic-nematic phase transition. This transition lies above the glass transition temperature one would extrapolate from the observed freezing behavior.

A fast algorithm for the exhaustive analysis of 12-nucleotide-long DNA sequences. Applications to human genomics

2004

We have developed a new algorithm that allows the exhaustive determination of words of up to 12 nucleotides in DNA sequences. It is fast enough as to be used at a genomic scale running on a standard personal computer. As an example, we apply the algorithm to compare the number of all 12-nucleotide long words in human chromosomes 21 and 22, each of them more than 33 million nucleotides long. Sequences that are chromosome specific are detected in less than 2 minutes, being analyzed any pair of chromosomes at a rate of 45 millions of nucleotides (45 Mb) per minute. The size of the words is long enough as to allow further analyses of all significant sequences using conventional database searche…

NMR spectral assignment of substituted salicylaldoximes by inverse pulse techniques withz-gradient selection: correlation of NMR parameters with subs…

1997

NMR Solution Conformation of the Proposed Recombin Like Structure D(CCGCGG)2

1997

Long repeated stretches of d(CCG) trinucleotide are the crucial mutation of gen that causes hereditary form of mental retardation (fragile X-syndrome). Moreover, the alternating (CG) dinucleotide is one of the candidates for Z-DNA conformation. Both sequences are part of the hexanucleotide d(CCGCGG)2- d(CCGCGG)2 forms different crystals depending on the crystallisation conditions. In one of these forms, the central alternating tetramer has a Z-DNA conformation, while the initial cytosine swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. In this communication a detailed comparison between solid and solution spatial conformation by NMR of …

1127P Correlation of BRAF mutation status in circulating tumour DNA (ctDNA) with tumour biopsy and clinical outcomes in COLUMBUS

2020

PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment

2017

The progress of next-generation sequencing has a major impact on medical and genomic research. This technology can now produce billions of short DNA fragments (reads) in a single run. One of the most demanding computational problems used by almost every sequencing pipeline is short-read alignment; i.e. determining where each fragment originated from in the original genome. Most current solutions are based on a seed-and-extend approach, where promising candidate regions (seeds) are first identified and subsequently extended in order to verify whether a full high-scoring alignment actually exists in the vicinity of each seed. Seed verification is the main bottleneck in many state-of-the-art a…