Prediction

PLPIHS – prediction of lncRNA-protein interactions using HeteSim scores

lncRNA

Massive studies have indicated that long non-coding RNAs (lncRNAs) are critical for the regulation of cellular biological processes by binding with RNA-related proteins. However, only a few experimentally supported lncRNA-protein associations have been reported. Existing network-based methods are typically focused on intrinsic features of lncRNA and protein but ignore the information implicit in the topologies of biological networks associated with ...

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A Review of Recent Computational Methods for Predicting Noncoding RNAs

lncrna

Noncoding RNAs (ncRNAs) play important roles in various cellular activities and diseases. Researchers from Hebei University of Science and Technology, present a comprehensive review on computational methods for ncRNA prediction, which are generally grouped into four categories: (1) homology-based methods, that is, comparative methods involving evolutionarily conserved RNA sequences and structures, (2) de novo methods using RNA sequence and structure features, ...

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RPI-Bind – a structure-based method for accurate identification of RNA-protein binding sites

lncRNA

RNA and protein interactions play crucial roles in multiple biological processes, while these interactions are significantly influenced by the structures and sequences of protein and RNA molecules. A large class of long noncoding RNAs (lncRNAs) can bind and modulate the activity of chromatin proteins, and play roles in chromatin modifications. In this process, lncRNAs, e.g. the Xist, with specific structures ...

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RIblast – An ultrafast RNA-RNA interaction prediction system for comprehensive lncRNA interaction analysis

lncRNA

Long non-coding RNAs (lncRNAs) play important roles in various biological processes. Although more than 58,000 human lncRNA genes have been discovered, most known lncRNAs are still poorly characterised. One approach to understanding the functions of lncRNAs is the detection of the interacting RNA target of each lncRNA. Because experimental detection of comprehensive lncRNA-RNA interactions are difficult, computational prediction of lncRNA-RNA ...

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COME – a robust coding potential calculation tool for lncRNA identification and characterization

lncrna

Recent genomic studies suggest that novel long non-coding RNAs (lncRNAs) are specifically expressed and far outnumber annotated lncRNA sequences. To identify and characterize novel lncRNAs in RNA sequencing data from new samples, researchers at Tsinghua University have developed COME, a coding potential calculation tool based on multiple features. It integrates multiple sequence-derived and experiment-based features using a decompose-compose method, which ...

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Computational Approaches for Functional Prediction and Characterisation of Long Noncoding RNAs

lncRNA

Although a considerable portion of eukaryotic genomes is transcribed as long noncoding RNAs (lncRNAs), the vast majority are functionally uncharacterised. The rapidly expanding catalogue of mechanistically investigated lncRNAs has provided evidence for distinct functional subclasses, which are now ripe for exploitation as a general model to predict functions for uncharacterised lncRNAs. By utilising publicly-available genome-wide datasets and computational methods, researchers ...

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IPMiner – to predict lncRNA-protein interactions

Non-coding RNAs (ncRNAs) play crucial roles in many biological processes, such as post-transcription of gene regulation. ncRNAs mainly function through interaction with RNA binding proteins (RBPs). To understand the function of a ncRNA, a fundamental step is to identify which protein is involved into its interaction. Therefore it is promising to computationally predict RBPs, where the major challenge is that ...

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DeepLNC, a long non-coding RNA prediction tool using a deep neural network

lncRNA

The significant role of long non-coding RNAs (lncRNAs) in various cellular functions, such as gene imprinting, immune response, embryonic pluripotency, tumorogenesis, and genetic regulations, has been widely studied and reported in recent years. Several experimental and computational methods involving genome-wide search and screenings of ncRNAs are being proposed utilizing sequence features-length, occurrence, and composition of bases with various limitations. Researchers ...

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lncRNATargets – A platform for lncRNA target prediction based on nucleic acid thermodynamics

lncRNA

Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. Researchers at the Peking Union Medical College have developed  lncRNATargets, which is a web-based platform for ...

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spongeScan – a graphical web tool for detecting microRNA binding elements in lncRNA sequences

lncRNA

Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, ...

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