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bioRxiv · 10.1101/327882

Characterization and identification of long non-coding RNAs based on feature relationship

Wang, G.·Yin, H.·Li, B.·Yu, C.·Wang, F.·Xu, X.·Cao, J.·Bao, Y.·Wang, L.·Abbasi, A.·Bajic, V.·Ma, L.·Zhang, Z.
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Abstract

The significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations. Here we first characterize lncRNAs by contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between ORF (open reading frame) length and GC content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.

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Wang, G., Yin, H., Li, B., Yu, C., Wang, F., Xu, X., Cao, J., Bao, Y., Wang, L., Abbasi, A., Bajic, V., Ma, L., Zhang, Z.. 2018-05-23. Characterization and identification of long non-coding RNAs based on feature relationship. https://doi.org/10.1101/327882

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