iSeeRNA: identification of long intergenic non-coding RNA transcripts from RNA-Seq data

Long intergenic non-coding RNAs (lincRNAs) are emerging as a novel class of non-coding RNAs and potent gene regulators. High-throughput RNA-sequencing combined with de novo assembly promises quantity discovery of novel transcripts. However, the identification of lincRNAs from thousands of assembled transcripts is still challenging due to the difficulties of separating them from protein coding transcripts (PCTs).

A team of scientists at The Chinese University of Hong Kong have developed iSeeRNA, a support vector machine (SVM)-based classifier for the identification of lincRNAs. iSeeRNA shows better performance compared to other software.

iSeeRNA demonstrates high prediction accuracy and runs several magnitudes faster than other similar programs. It can be integrated into the transcriptome data analysis pipelines or run as a web server, thus offering a valuable tool for lincRNA study.

Availability – iSeeRNA is available as a user-friendly web server with free accessibility at http://www.myogenesisdb.org/iSeeRNA

• Sun K, Chen X, Jiang P, Song X, Wang H, Sun H. (2013) iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics 14(supp 2). [article]