Computational Regulatory Genomics

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Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cis-NATs using ssRNA-seq, we developed a new computational method based on model comparison that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole root and cell-type specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified hundreds of additional cis-NAT pairs.

Song Li, Louisa Liberman, Neelanjan Mukherjee, Philip N. Benfey, Uwe Ohler. (2013). Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Research.

R version '2.15.2' or higher. R is a free and popular statistical software that can be downloaded here.
DESeq version '1.10.1'. DESeq is a bioconductor package for count data analysis using negative bionomial distribution. To install DESeq, follow the instruction here.
ROCR version '1.0.2'. ROCR is an R package for classifier visualization. Download ROCR here

Package Source for Linux Users: NASTIseq_1.0.tar.gz
Windows Users:


    • Download and install the required R, ROCR and DESeq package.
    • Download the source code for NASTIseq from the link above.
    • Linux:
      In the directory where you downloaded the source code, simply type "R CMD INSTALL NASTIseq_1.0.tar.gz".

      Or within an active R session, type:
      > install.packages('NASTIseq_1.0.tar.gz',repos=NULL,type='source')
      > library(NASTIseq)


  • Windows:
    From the pull-down menu, click on "Packages->Install Packages from local zip file", and then select the downloaded file


Download the README file, which is also included in the source package.

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