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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Data are individual items of information obtained from a population or sample. Data may be classified as qualitative (categorical), quantitative continuous, or quantitative discrete. Because it is not practical to measure the entire population in a study, researchers use samples to represent the population. A random sample is a representative group from the population chosen by using a method that gives each individual in the population an equal chance of being included in the sample. Random...
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When we take repeated measurements on the same or replicated samples, we will observe inconsistencies in the magnitude. These inconsistencies are called errors. To categorize and characterize these results and their errors, the researcher can use statistical analysis to determine the quality of the measurements and/or suitability of the methods.
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Biostatistics plays a crucial role in understanding and analyzing data in healthcare and biology. Biostatisticians conduct experiments, gather evidence, and draw meaningful conclusions using statistical methods and techniques. Different variables form the foundation of biostatistical analysis, allowing researchers to understand and interpret data effectively. These variables are classified into different types, each serving a specific purpose in statistical analysis.
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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
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EasyFigAssembler: Enhance Omics Data Storytelling through Effective Figure Assembly.

Nguyen Phuoc Long1,2, Nguyen Quang Thu1

  • 1Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan.

Journal of Proteome Research
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Summary

EasyFigAssembler simplifies creating complex multi-panel omics figures for publications. This web application accelerates figure assembly with smart layouts and quality checks, reducing errors and saving researchers time.

Keywords:
figure assemblingmultipanel figuresomics-based figuresquality advisorsmart layout

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Scientific Visualization

Background:

  • Multi-panel omics figures are crucial for data communication but complex to create.
  • Existing tools require specialized skills and are time-consuming.
  • A need exists for efficient and user-friendly omics figure assembly software.

Purpose of the Study:

  • To present EasyFigAssembler, a web application designed to simplify and accelerate the creation of multi-panel omics figures.
  • To provide a comprehensive solution for figure assembly without requiring programming expertise.
  • To enhance the quality and journal compliance of scientific figures.

Main Methods:

  • Developed a user-friendly web application, EasyFigAssembler.
  • Implemented features like nondestructive panel editing, project management, and high-resolution export.
  • Integrated a Smart Layout feature for automated panel arrangement.
  • Included advanced controls for complex layout creation and a Quality Advisor module.

Main Results:

  • EasyFigAssembler significantly simplifies and accelerates the assembly of multi-panel omics figures.
  • The application supports nondestructive editing, project management, and various export formats (TIFF, PDF, PNG, JPEG).
  • Smart Layout and advanced controls facilitate rapid creation of publication-ready, complex layouts.
  • The Quality Advisor ensures effective resolution and color-blind-friendly palettes for journal compliance.

Conclusions:

  • EasyFigAssembler offers a complete, efficient, and user-friendly solution for assembling complex omics-based figures.
  • The tool empowers researchers to create high-quality, publication-ready figures with reduced effort and errors.
  • EasyFigAssembler promotes better data visualization and adherence to journal standards in omics research.