Valentinetoft1974

Linearity of this method was achieved in the ranges of 4.00-40.00, 0.20-10.00 and 0.50-10.00 μg/mL for BHX, IMB and IMC, respectively. The validation of these chromatographic methods was made according to International Conference on Harmonization guidelines. These methods were successfully applied for determination of BHX in its pharmaceutical formulation. Also, statistical comparison was attained between the developed methods and the reported HPLC method using Student's t-test and F-test, and the obtained results showed that there was not any significant difference between them concerning with accuracy and precision.

Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet.

We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. https://www.selleckchem.com/B-Raf.html We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.

Source code and test data are available from https//gitlab.ub.uni-bielefeld.de/gi/plast.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

Many tools can reconstruct viral sequences based on next generation sequencing reads. Although existing tools effectively recover local regions, their accuracy suffers when reconstructing the whole viral genomes (strains). Moreover, they consume significant memory when the sequencing coverage is high or when the genome size is large. We present WgLink to meet this challenge. WgLink takes local reconstructions produced by other tools as input and patches the resulting segments together into coherent whole-genome strains. We accomplish this using an L0+L1-regularized regression synthesizing variant allele frequency data with physical linkage between multiple variants spanning multiple regions simultaneously. WgLink achieves higher accuracy than existing tools both on simulated and real data sets while using significantly less memory (RAM) and fewer CPU hours.

Source code and binaries are freely available at https//github.com/theLongLab/wglink.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

Compared with the second generation sequencing technologies, the third generation sequencing technologies allows us to obtain longer reads (average ∼10kbps, maximum 900kbps), but brings a higher error rate (∼15% error rate). Nanopolish is a variant and methylation detection tool based on Hidden Markov Model (HMM), which uses Oxford Nanopore sequencing data for signal-level analysis. Nanopolish can greatly improve the accuracy of assembly, whereas it is limited by long running time since most executive parts of Nanopolish is a serial and computationally expensive process.

In this paper, we present an effective polishing tool, Multithreading Nanopolish (MultiNanopolish), which decomposes the whole process of iterative calculation in Nanopolish into small independent calculation tasks, making it possible to run this process in the parallel mode. Experimental results show that MultiNanopolish reduces running time by 50% with read-uncorrected assembler (Miniasm) and 20% with read-corrected assembler (Canu and Flye) based on 40 threads mode compared to the original Nanopolish.

MultiNanopolish is available at GitHub https//github.com/BioinformaticsCSU/MultiNanopolish.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

Recent research has used the theory of planned behavior (TPB) to predict sleep. However, this research has focused on between-person effects and has failed to capture the intraindividual variability of sleep-related attitudes, subjective norms, perceived behavioral control, and intentions.

The current study sought to characterize the between- and within-day patterns of these constructs.

Participants (N = 79) completed a 1 week ecological momentary assessment protocol in which they reported their attitudes, subjective norms, perceived behavioral control, and intentions toward nightly sleep opportunity four times per day.

Analyses revealed both between- and within-day variability of these constructs, with perceived behavioral control and intentions demonstrating greater variability than attitudes and subjective norms. Mixed linear models revealed that attitudes and subjective norms significantly increased throughout the week, while perceived behavioral control and intentions significantly decreased throughout the day.

The between- and within-day patterns of the TPB constructs highlight important methodological considerations and provide insight into the potential refinement of sleep promotion efforts.

The between- and within-day patterns of the TPB constructs highlight important methodological considerations and provide insight into the potential refinement of sleep promotion efforts.

Genoscapist is a web-tool generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome datasets available for Bacillus subtilis and Staphylococcus aureus.

Websites and source code freely accessible at https//genoscapist.migale.inrae.fr.

Websites and source code freely accessible at https//genoscapist.migale.inrae.fr.