Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
By T. Carver, Matthew Berriman, Adrian R. N. Tivey, Chinmay Patel, U. Böhme, B. Barrell, Julian Parkhill, M. Rajandream. Bioinform., 2008
587 citations recorded by the source corpus.
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/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/8664bcd08e604d442aa0a8c6b2c9d25b29c66485
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In Molecular Biology
- Edith Gourbeyre
- Patricia Siguier
- Michael Chandler
- Matthew Berriman
- Paul Julian Kersey
- Andrew H. Paterson
- Thomas D. Otto
- R. Casu
Citations in the corpus
- PomBase: a comprehensive online resource for fission yeast (2011, methodology): “Sequence features are curated in Chado using Artemis (15,16).”
- The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome (2011, methodology): “Several other tools are connected to the database to query, compare and curate the automatic predictions (Artemis and ACT) ( Carver et al. 2008 ).”
- RATT: Rapid Annotation Transfer Tool (2011, methodology): “Further outputs include statistics about transferred features or the amount of synteny conserved between the reference and query, as well as Artemis-readable files showing SNPs, indels and regions that lack synteny between the compared sequences, see the example on the sourceforge site.”
- ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes (2011, methodology): “The corrected file can be exported to applications such as Artemis [13] and Gbrowser [14] for further analysis.”