ArticleEvolutionary bioinformatics online2013
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.
Article in Evolutionary bioinformatics online, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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88 citing papers in PubMed.
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28 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
backgroundThe 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.
resultsHere 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.
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