Introduction

BACKGROUND: RNA-seq and its variant differential RNA-seq (dRNA-seq) are today routine methods for transcriptome analysis in bacteria. While expression profiling and transcriptional start site prediction are standard tasks today, the problem of identifying transcriptional units in a genome-wide fashion is still not solved for prokaryotic systems. RESULTS: We present RNAseg, an algorithm for the prediction of transcriptional units based on dRNA-seq data. A key feature of the algorithm is that, based on the data, it distinguishes between transcribed and un-transcribed genomic segments. Furthermore, the program provides many different predictions in a single run, which can be used to infer the significance of transcriptional units in a consensus procedure. We show the performance of our method based on a well-studied dRNA-seq data set for Helicobacter pylori. CONCLUSIONS: With our algorithm it is possible to identify operons and 5'- and 3'-UTRs in an automated fashion. This alleviates the need for labour intensive manual inspection and enables large-scale studies in the area of comparative transcriptomics.

Publications

  1. Transcript mapping based on dRNA-seq data.
    Cite this
    Bischler T, Kopf M, Voß B, 2014-01-01 - BMC bioinformatics

Credits

  1. Thorsten Bischler
    Developer

  2. Matthias Kopf
    Developer

  3. Björn Voß
    Investigator

    Genetics & Experimental Bioinformatics, Institute for Biology 3

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Summary
AccessionBT005670
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByBjörn Voß