Project #2595
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#2595 : A program to identify integrons, attC sites and gene cassettes
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Name of Applicant : Eduardo Rocha
Date of application : 12-03-2015
Unit : Microbial Evolutionary Genomics
Location : Bat François Jacob, 6eme
Phone : 3353
@ Mail :

Project context and summary :

Integrons drive the spread of antibiotic resistance genes in bacterial populations. While their role is widely known (integron+antibiotic+resistance in PubMed gives > 1700 hits), there was no software available to identify integrons and their different components. We have made a script (in Python) which annotates DNA sequences (with prodigal), then identifies the integrase of the integron (using hmm protein profiles), searches attC sites (using covariance models from structurally annotated multiple sequence alignments of DNA sequences), searches certain types of promoters (string search using Python functions), and outputs all this and the genes in the cassettes (between attC sites). We would like the program to be available via Mobyle (or other convenient way) as a web server. Thus would facilitate its use by most biologists (which could still use the scripts if they wish to). It would also facilitate the publication of the methodological manuscript.

Related team publications :
Cury et al in preparation for NAR
Oliveira PH, Touchon M, Rocha EPC. (2014) The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucl Acids Res 42:10618-31
Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC, Murphy C, Feldgarden M, Wortman J, Clermont D, Lambert T, Grillot-Courvalin C, Nemec A, Courvalin P, Rocha EPC (2014) The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences. Genome Biol Evol 6:2866-2882.
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Project Type : Medium
Status : Closed
Publication : Automatic and accurate identification of integrons and cassette arrays in bacterial genomes reveals unexpected patterns Jean Cury, Thomas Jové, Marie Touchon, Bertrand Néron, Eduardo PC Rocha doi:
Global Satisfaction for this application : Excellent (5/5)

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