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Nucleic Acids Research 2006 34(Database Issue):D338-D343; doi:10.1093/nar/gkj060
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Nucleic Acids Research, 2006, Vol. 34, Database issue D338-D343
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

ICDS database: interrupted CoDing sequences in prokaryotic genomes

Emmanuel Perrodou, Caroline Deshayes1, Jean Muller, Christine Schaeffer2, Alain Van Dorsselaer2, Raymond Ripp, Olivier Poch, Jean-Marc Reyrat1 and Odile Lecompte*

Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP BP 163, 67404 Illkirch Cedex, France 1Inserm-UMR 570, Unité de Pathogénie des Infections Systémiques Groupe Avenir, Paris Cedex 15, F-75730, France 2Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO) UMR 7512, ECPM 25 rue Becquerel, Strasbourg F-67087 Cedex 2, France

*To whom correspondence should be addressed. Tel: +33 3 88 65 32 00; Fax: +33 3 88 65 32 01; Email: lecompte{at}igbmc.u-strasbg.fr

Received August 9, 2005. Revised October 5, 2005. Accepted October 5, 2005.

Unrecognized frameshifts, in-frame stop codons and sequencing errors lead to Interrupted CoDing Sequence (ICDS) that can seriously affect all subsequent steps of functional characterization, from in silico analysis to high-throughput proteomic projects. Here, we describe the Interrupted CoDing Sequence database containing ICDS detected by a similarity-based approach in 80 complete prokaryotic genomes. ICDS can be retrieved by species browsing or similarity searches via a web interface (http://www-bio3d-igbmc.u-strasbg.fr/ICDS/). The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. Furthermore, to facilitate the experimental characterization of ICDS, we propose optimized primers for re-sequencing purposes. The database will be regularly updated with additional data from ongoing sequenced genomes. Our strategy has been validated by three independent tests: (i) ICDS prediction on a benchmark of artificially created frameshifts, (ii) comparison of predicted ICDS and results obtained from the comparison of the two genomic sequences of Bacillus licheniformis strain ATCC 14580 and (iii) re-sequencing of 25 predicted ICDS of the recently sequenced genome of Mycobacterium smegmatis. This allows us to estimate the specificity and sensitivity (95 and 82%, respectively) of our program and the efficiency of primer determination.


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