title: FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.
abstract: Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc.
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Valentin
authors.initials: V
authors.lastname: Wucher
authors.affiliation: IGEPP, BIPAA, INRA, Campus Beaulieu, Le Rheu 35653, France.|Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes 35042, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Legeai
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Hédan
authors.affiliation: Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes 35042, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Rizk
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Lætitia
authors.initials: L
authors.lastname: Lagoutte
authors.affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland.
authors.forename: Tosso
authors.initials: T
authors.lastname: Leeb
authors.affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland.
authors.forename: Vidhya
authors.initials: V
authors.lastname: Jagannathan
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Edouard
authors.initials: E
authors.lastname: Cadieu
authors.affiliation: IGEPP, BIPAA, INRA, Campus Beaulieu, Le Rheu 35653, France.
authors.forename: Audrey
authors.initials: A
authors.lastname: David
authors.affiliation: Department of Veterinary Biosciences and Research Programs Unit, Molecular Neurology, University of Helsinki, PO Box 63, Helsinki 00014, Finland.|The Folkhälsan Institute of Genetics, Helsinki 00014, Finland.
authors.forename: Hannes
authors.initials: H
authors.lastname: Lohi
authors.affiliation: Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1870, Denmark.
authors.forename: Susanna
authors.initials: S
authors.lastname: Cirera
authors.affiliation: Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1870, Denmark.
authors.forename: Merete
authors.initials: M
authors.lastname: Fredholm
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Nadine
authors.initials: N
authors.lastname: Botherel
authors.affiliation: Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CM, the Netherlands.
authors.forename: Peter A J
authors.initials: PAJ
authors.lastname: Leegwater
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Le Béguec
authors.affiliation: Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CM, the Netherlands.
authors.forename: Hille
authors.initials: H
authors.lastname: Fieten
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Johnson
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Alföldi
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: André
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.|Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Hitte
authors.affiliation: Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Derrien
mesh_terms: D000818:Animals; D019985:Benchmarking; D003663:Decision Trees; D004285:Dogs; D005786:Gene Expression Regulation; D016678:Genome; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation / Q000379:methods* / Q000706:statistics & numerical data; D016366:Open Reading Frames; D062085:RNA, Long Noncoding / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000145:classification / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger