Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs lincRNAs - Application in Human Skeletal Muscle CellsReport as inadecuate




Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs lincRNAs - Application in Human Skeletal Muscle Cells - Download this document for free, or read online. Document in PDF available to download.

Ab initio assembly of transcriptome sequencing data has been widely used to identify large intergenic non-coding RNAs lincRNAs, a novel class of gene regulators involved in many biological processes. To differentiate real lincRNA transcripts from thousands of assembly artifacts, a series of filtering steps such as filters of transcript length, expression level and coding potential, need to be applied. However, an easy-to-use and publicly available bioinformatics pipeline that integrates these filters is not yet available. Hence, we implemented sebnif, an integrative bioinformatics pipeline to facilitate the discovery of bona fide novel lincRNAs that are suitable for further functional characterization. Specifically, sebnif is the only pipeline that implements an algorithm for identifying high-quality single-exonic lincRNAs that were often omitted in many studies. To demonstrate the usage of sebnif, we applied it on a real biological RNA-seq dataset from Human Skeletal Muscle Cells HSkMC and built a novel lincRNA catalog containing 917 highly reliable lincRNAs. Sebnif is available at http:-sunlab.lihs.cuhk.edu.hk-sebnif-.



Author: Kun Sun, Yu Zhao, Huating Wang, Hao Sun

Source: http://plos.srce.hr/



DOWNLOAD PDF




Related documents