title: Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans.
abstract: BACKGROUND
  Graphical representations of contrasts in GC usage among codon frame positions (frame analysis) provide evidence of genes missing from the annotations of prokaryotic genomes of high GC content but the qualitative approach of visual frame analysis prevents its applicability on a genomic scale.
  
  
  RESULTS
  We developed two quantitative methods for the identification and statistical characterization in sequence regions of three-base periodicity (hits) associated with open reading frame structures. The methods were implemented in the N-Profile Analysis Computational Tool (NPACT), which highlights in graphical representations inconsistencies between newly identified ORFs and pre-existing annotations of coding-regions. We applied the NPACT procedures to two recently annotated strains of the deltaproteobacterium Anaeromyxobacter dehalogenans, identifying in both genomes numerous conserved ORFs not included in the published annotation of coding regions.
  
  
  METHODS
  NPACT is available as a web-based service and for download at http://genome.ufl.edu/npact.
  
  
  BACKGROUND
  lucianob@ufl.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA and Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Oden
authors.affiliation: Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA and Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
authors.forename: Luciano
authors.initials: L
authors.lastname: Brocchieri
mesh_terms: D003062:Codon; D020862:GC Rich Sequence; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D009231:Myxococcales / Q000235:genetics*; D016366:Open Reading Frames; D012984:Software
chemical_list: D003062:Codon