Sökning: onr:"swepub:oai:gup.ub.gu.se/246335" >
HattCI: Fast and Ac...
HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models
-
- Buongermino Pereira, Mariana, 1982 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg
-
- Wallroth, Mikael (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,Chalmers tekniska högskola,Chalmers University of Technology
-
- Kristiansson, Erik, 1978 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology
-
visa fler...
-
- Axelson-Fisk, Marina, 1972 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology
-
visa färre...
-
(creator_code:org_t)
- Mary Ann Liebert Inc, 2016
- 2016
- Engelska.
-
Ingår i: Journal of Computational Biology. - : Mary Ann Liebert Inc. - 1066-5277 .- 1557-8666. ; 23:11, s. 891-902
- Relaterad länk:
-
http://dx.doi.org/10...
-
visa fler...
-
https://gup.ub.gu.se...
-
https://doi.org/10.1...
-
https://research.cha...
-
visa färre...
Abstract
Ämnesord
Stäng
- 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 http://bioinformatics.math.chalmers.se/HattCI.
Ämnesord
- NATURVETENSKAP -- Matematik (hsv//swe)
- NATURAL SCIENCES -- Mathematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- NATURVETENSKAP -- Matematik -- Sannolikhetsteori och statistik (hsv//swe)
- NATURAL SCIENCES -- Mathematics -- Probability Theory and Statistics (hsv//eng)
Nyckelord
- 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
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas