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Bioinformatics Advance Access published online on October 9, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn529
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Tim Carver 1,*, Matthew Berriman , Adrian Tivey , Chinmay Patel , Ulrike Böhme , Barclay G. Barrell , Julian Parkhill and Marie-Adele Rajandream

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

*To whom correspondence should be addressed. Dr. Tim Carver, E-mail: artemis{at}sanger.ac.uk


  Abstract

Motivation: Artemis and 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 addi-tion, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit func-tional annotation, based on standard ontologies, controlled vocabu-laries 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/

Contact: artemis{at}sanger.ac.uk

Associate Editor: Prof. John Quackenbush

Received on August 10, 2008; revised on September 19, 2008; accepted on October 6, 2008

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