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

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 lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together.

Example results page generated by lncRNATargets 

lncRNA

All results will be displayed in a table with green and red color according to the ΔG Threshold Value. Each row can be clicked to show the alignment diagrams.

Availability – lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/

Hu R, Sun X. (2016) lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics. J Bioinform Comput Biol [Epub ahead of print]. [abstract]

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