Article open access publication

FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome

Nucleic Acids Research, Oxford University Press (OUP), ISSN 0305-1048

Volume 45, 8, 2017

DOI:10.1093/nar/gkw1306, Dimensions: pub.1011303263, PMC: PMC5416892, PMID: 28053114,

Affiliations

Organisations

  1. (1) French National Centre for Scientific Research, grid.4444.0
  2. (2) Institut de Recherche en Informatique et Systèmes Aléatoires, grid.420225.3
  3. (3) Institute for Genetics, Environment and Plant Protection, grid.462490.d
  4. (4) University of Bern, grid.5734.5
  5. (5) University of Helsinki, grid.7737.4
  6. (6) University of Copenhagen, grid.5254.6, KU
  7. (7) Utrecht University, grid.5477.1
  8. (8) Broad Institute, grid.66859.34
  9. (9) Uppsala University, grid.8993.b

Description

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.

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Times Cited: 115

Field Citation Ratio (FCR): 24.17

Relative Citation ratio (RCR): 7.38

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