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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Updated: Jun 29, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

Tim Carver1, Matthew Berriman, Adrian Tivey

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

Bioinformatics (Oxford, England)
|October 11, 2008
PubMed
Summary
This summary is machine-generated.

Artemis and Artemis Comparison Tool (ACT) now support the GMOD Chado database schema, enabling annotation of complex genome sequences. A new Gene Builder tool enhances gene model editing and functional annotation capabilities.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Artemis and Artemis Comparison Tool (ACT) are widely used for sequence data viewing and annotation, especially for microbial genomes.
  • Previous versions were limited by flat file input/output, restricting the annotation of complex and large genome sequences.
  • Continuous development based on user feedback has driven enhancements in Artemis functionality.

Purpose of the Study:

  • To enhance the Artemis and ACT software by enabling direct interaction with relational database schemas.
  • To improve the annotation process for complex, large, and fragmented genome sequences.
  • To introduce a Gene Builder tool for structured editing of gene models and functional annotations.

Main Methods:

  • Extended Artemis and ACT to read and write directly to the Generic Model Organism Database (GMOD) Chado relational database schema.
  • Developed a Gene Builder tool with structured forms and tables for editing gene model coordinates.
  • Integrated standard ontologies, controlled vocabularies, and free text for functional annotation within Gene Builder.

Main Results:

  • Artemis and ACT can now directly utilize the GMOD Chado database schema for sequence data management.
  • The Gene Builder tool facilitates efficient editing of gene models and functional annotations.
  • The enhanced Artemis/ACT system supports the annotation of more complex and fragmented genome sequences.

Conclusions:

  • The integration with the GMOD Chado schema significantly expands the capabilities of Artemis and ACT for genome annotation.
  • The Gene Builder tool streamlines the process of refining gene models and functional descriptions.
  • These advancements provide a more robust platform for genomic research, particularly for large and intricate datasets.