A Few Tools For lncRNA Research

 With the development of technology and research, lncRNA started to play an important role in many research fields, especially the medical research. It is known that lncRNA is related to many diseases, so researchers started to do research on lncRNA.
Useful tools are necessary. Except the basic lncRNA sequencing technology, some analysis tools are also needed, such as some identification tools and gene location tools. Here I summarized some useful tools.

StarBase: http://starbase.sysu.edu.cn/
This platform is the most comprehensive internet system of miRNA, lncRNA, and circRNA based on the CLIP-Seq data. It constructs the regulatory network of ceRNA, and provides the identification tool of lncRNA. StarBase was published in 2011, and was quoted for hundred times.

StarScan: http://mirlab.sysu.edu.cn/starscan  
The identification software based on the degradome sequencing of different kinds of small RNA, target lncRNA, circRNA, pseudogen and mRNA of plants and animals. It has integrated degradome sequencing data of twenty kinds of species. StarScan can identify different types of target small RNA, which includes the lncRNA, circRNA encoding gene and pseudogene.

DIANA-LncBase: www.microrna.gr/LncBase
It is the regulation relationship of miRNA and lncRNA based on the single CLIP-Seq data and computational identification.

miRcode: http://www.mircode.org/mircode/
A software can identify target spot of miRNA which was invented by researchers from University of Gothenburg. It contains the integrated transcriptome annotated by GENECODE, including 10,419 registered lncRNA.

linc2GO: http://www.bioinfo.tsinghua.edu.cn/~liuke/Linc2GO/index.html
The functional annotation database of lncRNA created by Tsinghua University. However, the tools only based on computer will lead to high false positive. It can only be used as an auxiliary tool.

ChipBase: http://deepbase.sysu.edu.cn/chipbase/
You can find transcription factors which have regulation functions on lncRNA expression. If you want to have a look at the expression pattern of lncRNA in normal organism, you can check the expression pattern of lnRNA based on RNA-Seq in ChipBase(http://deepbase.sysu.edu.cn/chipbase/expression.php)

UCSC Genome Browse: http://genome.ucsc.edu/cgi-bin/hgGateway
If you know the chromosome location of the lncRNA, and you want to find the gene name of Ensembl/refSeq and gene symbol. If you are not familiar with it, you can try the software of UCSC, blat( http://genome.ucsc.edu/cgi-bin/hgBlat?command=start ). And if you want to learn how to used the UCSC Genome Browser, you can find it here: http://www.openhelix.com/ucsc