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About the Authors:
Leander Schietgat
Roles Formal analysis, Investigation, Methodology, Writing - original draft
Affiliation: Department of Computer Science, KU Leuven, Leuven, Belgium
Celine Vens
Roles Conceptualization, Formal analysis, Methodology, Writing - original draft
* E-mail: [email protected]
Affiliations Department of Computer Science, KU Leuven, Leuven, Belgium, Department of Public Health and Primary Care, KU Leuven Kulak, Kortrijk, Belgium, Department of Respiratory Medicine, Ghent University, and VIB Inflammation Research Center, Ghent, Belgium
ORCID http://orcid.org/0000-0003-0983-256X
Ricardo Cerri
Roles Formal analysis, Methodology, Validation, Writing - original draft
Affiliation: Department of Computer Science, UFSCar Federal University of São Carlos, São Carlos, São Paulo, Brazil
ORCID http://orcid.org/0000-0002-2582-1695
Carlos N. Fischer
Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Methodology, Project administration, Writing - original draft
Affiliation: Department of Statistics, Applied Mathematics, and Computer Science, UNESP São Paulo State University, Rio Claro, São Paulo, Brazil
ORCID http://orcid.org/0000-0002-5598-6263
Eduardo Costa
Roles Formal analysis, Investigation, Methodology, Writing - review & editing
Affiliations Department of Computer Science, KU Leuven, Leuven, Belgium, Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, São Carlos, São Paulo, Brazil
Jan Ramon
Roles Conceptualization, Funding acquisition, Methodology, Project administration, Supervision, Writing - review & editing
Affiliations Department of Computer Science, KU Leuven, Leuven, Belgium, INRIA Lille Nord Europe, 40 avenue Halley, 59650 Villeneuve d’Ascq, France
Claudia M. A. Carareto
Roles Conceptualization, Methodology, Validation, Writing - review & editing
Affiliation: Department of Biology, UNESP São Paulo State University, São José do Rio Preto, São Paulo, Brazil
Hendrik Blockeel
Roles Conceptualization, Funding acquisition, Project administration, Supervision, Writing - review & editing
Affiliation: Department of Computer Science, KU Leuven, Leuven, Belgium
ORCID http://orcid.org/0000-0003-0378-3699Abstract
Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. Accurate identification and classification of TEs present in a genome is an important step towards understanding their effects on genes and their role in genome evolution. We introduce TE-Learner, a framework based on machine learning that automatically identifies TEs in a given genome and assigns a classification to them. We present an implementation of our framework towards LTR retrotransposons, a particular type of TEs characterized by having long terminal repeats (LTRs)...