This article is part of the supplement: European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Leading applications and technologies in bioinformatics

Open Access Proceedings

The Mycoplasma conjunctivae genome sequencing, annotation and analysis

Sandra P Calderon-Copete1, George Wigger2, Christof Wunderlin2, Tobias Schmidheini2, Joachim Frey3, Michael A Quail4 and Laurent Falquet1*

Author Affiliations

1 Swiss Institute of Bioinformatics, Génopode-UNIL, 1015 Lausanne, Switzerland

2 Microsynth AG, Schützenstrasse 15, P.O. Box, 9436 Balgach, Switzerland

3 Institute for Veterinary Bacteriology, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland

4 Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK

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BMC Bioinformatics 2009, 10(Suppl 6):S7  doi:10.1186/1471-2105-10-S6-S7

Published: 16 June 2009



The mollicute Mycoplasma conjunctivae is the etiological agent leading to infectious keratoconjunctivitis (IKC) in domestic sheep and wild caprinae. Although this pathogen is relatively benign for domestic animals treated by antibiotics, it can lead wild animals to blindness and death. This is a major cause of death in the protected species in the Alps (e.g., Capra ibex, Rupicapra rupicapra).


The genome was sequenced using a combined technique of GS-FLX (454) and Sanger sequencing, and annotated by an automatic pipeline that we designed using several tools interconnected via PERL scripts. The resulting annotations are stored in a MySQL database.


The annotated sequence is deposited in the EMBL database (FM864216) and uploaded into the mollicutes database MolliGen webcite allowing for comparative genomics.


We show that our automatic pipeline allows for annotating a complete mycoplasma genome and present several examples of analysis in search for biological targets (e.g., pathogenic proteins).