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HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models

Journal article
Authors Mariana Buongermino Pereira
Mikael Wallroth
Erik Kristiansson
Marina Axelson-Fisk
Published in Journal of Computational Biology
Volume 23
Issue 11
Pages 891-902
ISSN 1066-5277
Publication year 2016
Published at Department of Mathematical Sciences
Pages 891-902
Language en
Keywords antibiotic resistance, hidden Markov model (HMM), horizontal gene transfer, mobile genetic elements, motif finding, mobile gene cassettes, antibiotic-resistance, 59-base element, integrons, recombination, dna, metagenomics, integrases, spread, binds, Biochemistry & Molecular Biology, Biotechnology & Applied Microbiology, Computer Science, Mathematical & Computational Biology, Mathematics
Subject categories Mathematics


Integrons are genetic elements that facilitate the horizontal gene transfer in bacteria and are known to harbor genes associated with antibiotic resistance. The gene mobility in the integrons is governed by the presence of attC sites, which are 55 to 141-nucleotide-long imperfect inverted repeats. Here we present HattCI, a new method for fast and accurate identification of attC sites in large DNA data sets. The method is based on a generalized hidden Markov model that describes each core component of an attC site individually. Using twofold cross-validation experiments on a manually curated reference data set of 231 attC sites from class 1 and 2 integrons, HattCI showed high sensitivities of up to 91.9% while maintaining satisfactory false-positive rates. When applied to a metagenomic data set of 35 microbial communities from different environments, HattCI found a substantially higher number of attC sites in the samples that are known to contain more horizontally transferred elements. HattCI will significantly increase the ability to identify attC sites and thus integron-mediated genes in genomic and metagenomic data. HattCI is implemented in C and is freely available at

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