FEELnc – a tool for long non-coding RNA annotation

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, researchers from University Rennes1 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. The researchers 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.

FEELnccodpot and FEELncclassifier description

lncRNA

(A) Two graph ROC curves for automatic detection of optimized CPS threshold and user specificity threshold, the latter defining two conservative sets of lncRNAs and mRNAs and a class of transcripts with ambiguous biotypes termed TUCp (Transcripts of Unknown Coding potential). B) Sub classification of intergenic and genic lncRNA/transcripts interactions by the FEELncclassifier module.

Availability – FEELnc is freely available at: https://github.com/tderrien/FEELnc

Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, Cirera S, Fredholm M, Botherel N, Leegwater PA, Le Béguec C, Fieten H, Johnson J, Alföldi J, André C, Lindblad-Toh K, Hitte C, Derrien T. (2017) FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res [Epub ahead of print]. [article]

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