title: EC2KEGG: a command line tool for comparison of metabolic pathways.
abstract: BACKGROUND
  Next-generation sequencing and metagenome projects yield a large number of new genomes that need further annotations, such as identification of enzymes and metabolic pathways, or analysis of metabolic strategies of newly sequenced species in comparison to known organisms. While methods for enzyme identification are available, development of the command line tools for high-throughput comparative analysis and visualization of identified enzymes is lagging.
  
  
  METHODS
  A set of perl scripts has been developed to perform automated data retrieval from the KEGG database using its new REST program application interface. Enrichment or depletion in metabolic pathways is evaluated using the two-tailed Fisher exact test followed by Benjamini and Hochberg correction.
  
  
  RESULTS
  Comparative analysis of a given set of enzymes with a specified reference organism includes mapping to known metabolic pathways, finding shared and unique enzymes, generating links to visualize maps at KEGG Pathway, computing enrichment of the pathways, listing the non-mapped enzymes.
  
  
  CONCLUSIONS
  EC2KEGG provides a platform independent toolkit for automated comparison of identified sets of enzymes from newly sequenced organisms against annotated reference genomes. The tool can be used both for manual annotations of individual species and for high-throughput annotations as part of a computational pipeline. The tool is publicly available at http://sourceforge.net/projects/ec2kegg/.
authors.affiliation: Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Porollo