RNA-Sequencing combined with ab initio assembly promise quantity discovery of novel transcripts including protein coding transcripts (mRNAs) as well as non-coding RNAs. However, the identification of large intergenic non-coding RNAs (lincRNAs), a novel class of potent regulators of gene expression, from thousands of assembled transcripts is still challenging due to the difficulties of separating them from mRNAs. To date, no software has been developed specifically for distinguishing lncRNAs from mRNAs despite the existence of several programs for ncRNAs (mainly for small ncRNAs) in general.

We thus implemented iSeeRNA for high throughput screening of lincRNAs from transcriptome sequencing data. We provided not only a user friendly web server but also a stand-alone program that can be integrated into a bioinformatics pipeline for complex transcriptome data analysis. The package is implemented in Perl/C++ and runs on most of the platforms supported by Linux/Unix.

Please refer to the download page to download stand-alone iSeeRNA.

Go to the webserver to run iSeeRNA on our webserver.
(More than 3000 web queries had been processed by Oct 31, 2016 :~)

*** If you are using RNA-seq coupled with ab initio assembly for novel lincRNA discovery, we strongly recommend you try our sebnif package for comprehensive filtering towards building the high quality novel lincRNA catalog. Find it out now! ***

Citation

When referencing, please cite "Sun et al.: iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics 2013 14(Suppl 2):S7."   PubMed   Full Paper