Elsevier

Tuberculosis

Volume 91, Issue 1, January 2011, Pages 8-13
Tuberculosis

Molecular Aspects
The MycoBrowser portal: A comprehensive and manually annotated resource for mycobacterial genomes

https://doi.org/10.1016/j.tube.2010.09.006Get rights and content

Summary

In this paper, we present the MycoBrowser portal (http://mycobrowser.epfl.ch/), a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. A central component of MycoBrowser is TubercuList (http://tuberculist.epfl.ch), which has recently benefited from a new data management system and web interface. These improvements were extended to all MycoBrowser databases. We provide an overview of the functionalities available and the different ways of interrogating the data then discuss how both the new information and the latest features are helping the mycobacterial research communities.

Introduction

Mycobacteria have plagued humanity for millennia by causing major diseases like tuberculosis, leprosy and Buruli ulcer. In terms of disease burden and mortality, tuberculosis is incontestably the most important and challenging threat, partly because of the increasing prevalence of primary resistance to the current drugs. There is thus a great need for new compounds with a novel mode of action1 and these may also find application in treating other mycobacterial diseases. Thanks to the control measures implemented by the World Health Organisation, leprosy is nearing elimination as a public health problem,2 while the emerging disease, Buruli ulcer, is of growing concern.3

In the past decade, genomics has played an important role in underpinning mycobacterial research by providing new information and knowledge about Mycobacterium tuberculosis,4 Mycobacterium leprae5 and Mycobacterium ulcerans,6 the etiologic agents of tuberculosis, leprosy and Buruli ulcer, respectively. The genome sequence of Mycobacterium marinum,7 an occasional human pathogen, revealed a very close relationship between this organism and M. ulcerans, while establishing a more distant link to M. tuberculosis. For the latter reason, M. marinum, although predominantly pathogenic for fish and amphibia, is finding application as a model for tuberculosis.

Shortly after publication of the genome sequence of M. tuberculosis H37Rv the annotations were made available through TubercuList, a relational database (http://genolist.pasteur.fr/TubercuList/).8 There is no doubt that the availability of the complete genome sequence and TubercuList has greatly helped the scientific community to study tuberculosis, as have related mycobacterial genomes and their cognate datasets. Previously sited at the Institut Pasteur, TubercuList has been relocated and is now hosted by the Ecole Polytechnique Fédérale de Lausanne (EPFL), where the website has been completely redesigned. Encouraged by the flexibility and popularity of this new format, we have extended it by developing the MycoBrowser portal (http://mycobrowser.epfl.ch). MycoBrowser provides whole genome sequences and related information from M. tuberculosis, M. leprae and M. marinum and incorporates a suite of search functions that are described below.

Section snippets

Software

The first generation of TubercuList used the relational database management system SYBASE. In keeping with recent trends in informatics in academia we adopted the PostgreSQL database engine, an open source object-relational database system, which runs on all major operating systems and has a strong reputation for reliability, data integrity, and correctness (http://www.postgresql.org/). We also redesigned the TubercuList web interface in PHP (http://php.net/), a recent, efficient, and

MycoBrowser website

Following its relocation, the TubercuList database has been substantially rewritten and a new web interface has been implemented. Such re-implementation was needed to make the resource more flexible by facilitating the development and integration of novel tools often as modules. In addition, flexible software design permits easy assimilation of new data sets that respond to user requests. For example, many users found it very convenient to have all the information about a single gene, ranging

Acknowledgements

We are grateful to the many users of our website for precious feedback and input, especially to Pushpendra Singh for the M. leprae data and to Tim Stinear for M. marinum. We thank Fabrice David from the EPFL for developing the 3D structure viewer.

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