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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred irrespective...
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IdBean: a Java GUI application for conversion of biological identifiers.

Sanghyuk Lee1, Bumjin Kim, Hyeonjin Kim

  • 1Lee Gil Ya Cancer and Diabetes Institute, Gachon University of Medicine and Science, Incheon 406-840, Korea.

BMB Reports
|February 25, 2011
PubMed
Summary
This summary is machine-generated.

IdBean is a Java GUI application that simplifies biological ID conversion by integrating multiple services. It enables direct merging and comparison of results, reducing errors and providing up-to-date information for gene analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biologists frequently encounter challenges with diverse biological identifiers (IDs) across different databases and analyses.
  • Manual conversion and reconciliation of gene or gene product IDs from multiple sources is time-consuming and error-prone.
  • Existing tools often lack integrated support for comparing or merging results from various ID conversion services.

Purpose of the Study:

  • To develop a user-friendly, stand-alone Java GUI application named IdBean for efficient biological ID conversion.
  • To integrate multiple widely-used ID conversion services that offer programmatic access.
  • To provide a novel solution for direct merging and comparison of conversion results from disparate services.

Main Methods:

  • Development of a biologist-friendly, stand-alone Java GUI application.
  • Integration of multiple existing ID conversion services with programmatic access.
  • Implementation of functionalities for direct merging and comparison of conversion outcomes.
  • Modular design allowing for repackaging into plug-in modules or integration into other bioinformatics tools.

Main Results:

  • IdBean successfully integrates numerous widely-used ID conversion services.
  • The application facilitates direct merging and comparison of conversion results without manual intervention.
  • It demonstrably reduces the number of failed IDs by leveraging multiple conversion sources.
  • Provides access to potentially up-to-date conversion results via online services.

Conclusions:

  • IdBean offers a significant advancement for biologists dealing with multiple gene or gene product ID types.
  • The tool streamlines ID conversion, enhancing the accuracy and efficiency of biological data analysis.
  • Its modular design supports broader applications within bioinformatics tool development.