The Microbe browser for comparative genomics

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Abstract

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five software packages. The Microbe browser is daily updated from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data are displayed in an easy-to-use, interactive website based on Ensembl software. The Microbe browser is available at http://microbe.vital-it.ch/. Programmatic access is available through the OMA application programming interface (API) at http://microbe.vital-it.ch/api.

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Most cited references 14

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Distinguishing homologous from analogous proteins.

W. M. Fitch (1970)

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Ensembl 2009

T. J. P. Hubbard, B. L. Aken, S. Ayling … (2009)

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

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Is Open Access

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

Tim Carver, Matthew Berriman, Adrian Tivey … (2008)

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.

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Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Journal ID (hwp): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: 1 July 2009

Publication date (Print): 1 July 2009

Publication date (Electronic): 30 April 2009

Publication date PMC-release: 30 April 2009

Volume: 37

Issue: Web Server issue

Pages: W296-W299

Affiliations

¹Swiss Institute of Bioinformatics (SIB), ²School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, ³Institute of Computational Science, ETH Zürich, 8092 Zürich and ⁴Vital-IT, Bâtiment Génopode, Université de Lausanne, 1015 Lausanne, Switzerland

Author notes

*To whom correspondence should be addressed. Tel: +41 21 693 9573; Fax: +41 21 693 1850; Email: jacques.rougemont@ 123456epfl.ch

Article

Publisher ID: gkp268

DOI: 10.1093/nar/gkp268

PMC ID: 2703916

PubMed ID: 19406928

SO-VID: 31b619d4-177b-4697-b46d-938daf70bc53

License:

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.

History

Date received : 27 January 2009

Date revision received : 3 April 2009

Date accepted : 11 April 2009

The Microbe browser for comparative genomics

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Abstract

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Arabidopsis genomics

Most cited references 14

Distinguishing homologous from analogous proteins.

Ensembl 2009

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

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