EDGE-pro: Eestimated Degree of Gene Expression in prokaryotic genomes

Tanja Magoc, Derrick Wood, Steven L. Salzberg

Research output: Contribution to journalArticlepeer-review

72 Scopus citations


Background: The expression levels of bacterial genes can be measured directly using next-generation sequencing (NGS) methods, offering much greater sensitivity and accuracy than earlier, microarray-based methods. Most bioinformatics software for estimating levels of gene expression from NGS data has been designed for eukaryotic genomes, with algorithms focusing particularly on detection of splicing patterns. These methods do not perform well on bacterial genomes. Results: Here we describe the first software system designed explicitly for quantifying the degree of gene expression in bacteria and other prokaryotes. EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) processes the raw data from an RNA-seq experiment on a bacterial or archaeal species and produces estimates of the expression levels for each gene in these gene-dense genomes. Software: The EDGE-pro tool is implemented as a pipeline of C++ and Perl programs and is freely available as open-source code at http://www.genomics.jhu.edu/software/EDGE/index.shtml.

Original languageEnglish (US)
Pages (from-to)127-136
Number of pages10
JournalEvolutionary Bioinformatics
Issue number9
StatePublished - Mar 10 2013


  • Bacteria
  • Gene expression
  • Prokaryotes
  • RNA-seq

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications


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