LncADeep: An ab initio lncRNA identification and functional annotation tool based on deep learning
===================================================================

Introduction
------------

Long noncoding RNAs (lncRNAs) play important biological roles and have been implicated in human diseases. To characterize lncRNAs, identifying and annotating lncRNAs is necessary. Here, we propose a novel lncRNA identification and functional annotation tool named **LncADeep**. First, **LncADeep** identifies lncRNAs by integrating sequence intrinsic and homology features based on deep belief networks. Second, **LncADeep** predicts lncRNA-protein interactions using sequence and structure features based on deep neural networks. Third, since accurate lncRNA-protein interactions can help to infer the functions of lncRNAs, **LncADeep** conducts KEGG and Reactome pathway enrichment analysis and functional module detection with the predicted interacting proteins of lncRNAs. Case studies show that LncADeep's annotations for lncRNAs comply with their known functions. As a tool for lncRNA identification and functional annotation based on deep learning, **LncADeep** has outperformed state-of-the-art tools on predicting lncRNAs and lncRNA-protein interactions, and can automatically provide informative functional annotations for lncRNAs.

**LncADeep** is freely available for non-commercial use at [http://cqb.pku.edu.cn/ZhuLab/LncADeep](http://cqb.pku.edu.cn/ZhuLab/LncADeep) or [https://github.com/cyang235/LncADeep](https://github.com/cyang235/LncADeep).

Version
-------
+ LncADeep 1.0 

Usage
-----
	-h --help		show this help message and exit

	-mt --modeltype	{full,partial}
					the model used for lncRNA identification,
					choose from partial full default is partial
					default is "partial".
					
	-HMM --HMMthread
					the thread number of using HMMER, default is 8
					
	-p --species	{human,mouse}
					the model of the species to choose (human,mouse).
					 default is "human".

	-t --thread		THREAD
                    The number of threads for running the LncADeep
					program.default is 8.

**example**
	ezLncPred LncADeep -h
	ezLncPred -i example.fa -o results LncADeep
	ezLncPred -i example.fa -o results LncADeep -mt full
	ezLncPred -i example.fa -o results LncADeep -HMM 4
	ezLncPred -i example.fa -o results LncADeep -p human
	ezLncPred -i example.fa -o results LncADeep -t 4

Citation
--------
[Cheng Yang, Longshu Yang, Man Zhou, Haoling Xie, Chengjiu Zhang, May D. Wang, and Huaiqiu Zhu. LncADeep: An ab initio lncRNA identification and annotation tool based on deep learning. (submitted, 2017)](to be added)


Contact
-------
Please direct your questions to: Dr. Huaiqiu Zhu, [hqzhu@pku.edu.cn](hqzhu@pku.edu.cn)
 
