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  • Director of Center
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Starting Date
02
Nov 2015
Ending Date
30
Nov 2017
Status
Ongoing
Members
3
Structures
2

About

IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (Galaxy), or by command line (IntegronFinder on github).

Integrons are major genetic element, notorious for their major implication in the spread of antibiotic resistance genes. More generally,  integrons are gene-capturing device, whose broader evolutionary role remains poorly understood. IntegronFinder is able to detect with high accuracy integron in DNA sequences. It is accurate because it combines the use of HMM profiles for the detection of the essential protein, the site-specific integron integrase, and the use of Covariance Models for the detection of the recombination site, the attC site.

IntegronFinder can also annotate gene cassettes (CDS nearby attC sites) using Resfams, a database of HMM profiles aiming at annotating antibiotic resistance genes. This database is provided but the user can add any other HMM profiles database of its own interest.

Authors: Jean Cury, Bertrand Néron and Eduardo Rocha

Availibility:

Documentation: IntegronFinder Documentation

Reference:

Identification and analysis of integrons and cassette arrays in bacterial genomes
Jean Cury; Thomas Jove; Marie Touchon; Bertrand Neron; Eduardo PC Rocha
Nucleic Acids Research 2016;
doi: 10.1093/nar/gkw319

Fundings