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

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Valentin Wucher, Fabrice Legeai, Benoît Hédan, Guillaume Rizk, Laetitia Lagoutte, Tosso Leeb, Vidhya Jagannathan, Edouard Cadieu, Audrey David, Hannes Lohi, Susanna Cirera Salicio, Merete Fredholm, Nadine Botherel, Peter A.J. Leegwater, Céline Le Béguec, Hille Fieten, Jeremy J Johnson, Jessica Alföldi, Catherine André, Kerstin Lindblad-Toh & 2 andre Christophe Hitte, Thomas Derrien

Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing andmonitoring 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.

OriginalsprogEngelsk
Artikelnummere57
TidsskriftNucleic Acids Research
Vol/bind45
Tidsskriftsnummer8
Antal sider12
ISSN0305-1048
DOI
StatusUdgivet - 2017

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