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

• DOI: 10.1093/bioinformatics/btn529
• Publication Date: 2008-10-10T00:34:47Z
• Authors: Tim Carver; Matthew Berriman; Adrian Tivey; Chinmay Patel; Ulrike Böhme; Barclay G. Barrell; Julian Parkhill; Marie-Adèle Rajan...
• Keywords: File format; Schema (genetic algorithms); Download

Abstract Motivation: Artemis and Comparison Tool (ACT) have become mainstream tools for viewing annotating sequence data, particularly microbial genomes. Since its first release, has been continuously developed supported with additional functionality editing analysing sequences based on feedback from an active user community of laboratory biologists professional annotators. Nevertheless, utility somewhat restricted by limitation to reading writing flat files. Therefore, a new version developed, which reads writes relational database schema, allows users annotate more complex, often large fragmented, genome sequences. Results: ACT now extended read write directly the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado schema. In addition, Gene Builder tool provide structured forms tables edit coordinates gene models functional annotation, standard ontologies, controlled vocabularies free text. Availability: are freely available (under GPL licence) download (for MacOSX, UNIX Windows) at Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/http://www.sanger.ac.uk/Software/ACT/ Contact: [e-mail] Supplementary information: data Bioinformatics online.