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

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/

Fig. 1.

Download statistics for Artemis and ACT for each year from 2001–2007.

Fig. 2.

The Artemis database and file manager. The organisms in the database are shown at the top. Double clicking on the chromosome opens it up in Artemis. The file management system also provides access to local (middle panel) and remote file systems (via ssh; bottom panel).

Fig. 3.

Snapshot of Artemis in database mode displaying chromosome 1 of P. falciparum. The sequence and feature displays are identical to the standard Artemis. There is a ‘Commit’ button at the top right of the interface for writing back to the database. The top feature display panel shows a zoomed-out representation of the region. Below this is a zoomed-in view showing the nucleotide level with the six frames of translation. The lower panel shows a scrollable list of the features. These panels are all linked, so that if a feature is selected by double clicking on it the other windows scroll to the feature. The polypeptide and transcript are hidden from the feature display but appear (greyed out) in the feature list at the bottom.

Fig. 4.

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

Fig. 5.

An example of a Protein Map in the Gene Builder. The details of the domain predictions are shown in mouse-over tool-tips. The protein database features (e.g. Pfam, Prosite) can be clicked on to open that entry in a browser window.

Fig. 6.

Example of a gene with multiple transcripts in the graphical view of the gene hierarchy in the Gene Builder. Each transcript is a child node of the gene in the tree on the left with its associated features displayed when expanded. To assist in building multiple transcripts the checkboxes to the left of each transcript are used to hide and show them in the main Artemis window.

Fig. 7.

Snapshot of the Artemis log viewer, using log4j to generate log messages and errors. It records SQL statements and can be used to monitor changes to the database. The last seven lines in this log are generated to show the changes made to the database in a more human readable format.