Skip Navigation



Bioinformatics Advance Access published online on October 9, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn529
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
24/23/2672    most recent
btn529v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Carver, T.
Right arrow Articles by Rajandream, M.-A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Carver, T.
Right arrow Articles by Rajandream, M.-A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
A. Gattiker, C. Dessimoz, A. Schneider, I. Xenarios, M. Pagni, and J. Rougemont
The Microbe browser for comparative genomics
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W296 - W299.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. S. P. Horler and C. K. Vanderpool
Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence
Nucleic Acids Res., June 16, 2009; (2009) gkp501v1.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.