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Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrell BG, Parkhill J, Rajandream MA - Bioinformatics (2008)

Bottom Line: Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators.Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files.Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences.

View Article: PubMed Central - PubMed

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

ABSTRACT

Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences.

Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text.

Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/

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The Gene Builder showing a gene hierarchy at the top and underneath the annotation for the associated polypeptide.
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Figure 4: The Gene Builder showing a gene hierarchy at the top and underneath the annotation for the associated polypeptide.

Mentions: A Gene Builder window for a selected gene feature can be opened from the ‘Edit’ menu by selecting the ‘Selected Feature in Editor’ option. The gene structure and feature annotation are two distinct parts of the Gene Builder (Fig. 4), and are described below. In general the majority of the annotation is attached to the polypeptide, although the system allows annotation to any object within the gene hierarchy. Therefore when a CDS is selected, and the Gene Builder opened for the corresponding gene, it displays the annotation on the polypeptide.Fig. 4.


Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrell BG, Parkhill J, Rajandream MA - Bioinformatics (2008)

The Gene Builder showing a gene hierarchy at the top and underneath the annotation for the associated polypeptide.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2606163&req=5

Figure 4: The Gene Builder showing a gene hierarchy at the top and underneath the annotation for the associated polypeptide.
Mentions: A Gene Builder window for a selected gene feature can be opened from the ‘Edit’ menu by selecting the ‘Selected Feature in Editor’ option. The gene structure and feature annotation are two distinct parts of the Gene Builder (Fig. 4), and are described below. In general the majority of the annotation is attached to the polypeptide, although the system allows annotation to any object within the gene hierarchy. Therefore when a CDS is selected, and the Gene Builder opened for the corresponding gene, it displays the annotation on the polypeptide.Fig. 4.

Bottom Line: Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators.Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files.Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences.

View Article: PubMed Central - PubMed

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

ABSTRACT

Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences.

Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text.

Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/

Show MeSH