8 papers · ranked by Valyu relevance
Federico Di Petta, Piermichele Rosati, Piero Hierro Canchari, Michela Quadrini + 1 more
Accurate annotation of RNA base-pairing interactions is essential for structural analysis, benchmarking, and data-driven RNA structure prediction. Several tools can extract RNA interactions from three-dimensional coordinates, but their outputs are heterogeneous and may disagree, particularly for non-canonical base…
Orges Koci, Richard K. Russell, M. Guftar Shaikh, Christine Edwards + 2 more
We have developed CViewer, a java-based framework to consolidate, visualize, and explore enormous amount of information recovered from shotgun sequencing experiments. This information includes and integrates all levels of gene products, mRNA, protein, metabolites, as well as their interactions in a single platform. The…
Olivia W Lang, Benjamin Beer, Dean Zhang, Courtney LeSon + 3 more
The growing diversity of genomic and epigenomic assays has driven a parallel expansion in data formats, analysis workflows, and figure-generation tools. However, tools for analyzing data and assembling publication-quality figures are often specialized to a specific assay, dramatically limiting their interoperability…
Caterina Fuster-Barceló, Carlos García López de Haro, Estibaliz Gómez-de-Mariscal, Wei Ouyang + 3 more
This manuscript showcases the latest advancements in deepImageJ, a pivotal Fiji/ImageJ plugin for bioimage analysis in the life sciences. The plugin, known for its user-friendly interface, facilitates the application of diverse pre-trained neural networks to custom data. The manuscript demonstrates a number of…
Rafael Gonçalves, Anderson Santos
Genome sequencing and assembly are trivial tasks nowadays. After assembling contigs and scaffolds from a genome, the subsequent step is annotation. An annotation evidencing the expected features, like rRNA, tRNA, and CDS, is a signal of the quality of our sequencing and assembly. Different techniques to obtain and…
Göksel Mısırlı
The Synthetic Biology Open Language version 3 data standard provides a graph-based approach to exchange information about biological designs. The new data model has major updates and offers several features for software tools. Here, we present libSBOLj3 to facilitate data exchange and provide interoperability between…
Chris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche + 4 more
Mass spectrometry is a powerful technique for analyzing molecules in complex biological samples. However, inter- and intra-laboratory variability and bias can affect the data due to various factors, including sample handling and preparation, instrument calibration and performance, and data acquisition and processing.…
Roberto Reinosa Fernández
The identification and analysis of open reading frames (ORFs) are fundamental steps in genome annotation, which requires accurate bioinformatics tools. OrfViralScan 3.0 is presented, a desktop application developed in Java (requires Java 11 to run), featuring an intuitive graphical user interface (GUI) designed to…