title: Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function.
abstract: BACKGROUND
  The process of translation can be affected by the use of rare versus common codons within the mRNA transcript.
  
  
  RESULTS
  Here, we show that rare codons are enriched at the 5' and 3' termini of genes from E. coli and other prokaryotes. Genes predicted to be secreted show significant enrichment in 5' rare codon clusters, but not 3' rare codon clusters. Surprisingly, no correlation between 5' mRNA structure and rare codon usage was observed.
  
  
  CONCLUSIONS
  Potential functional roles for the enrichment of rare codons at terminal positions are explored.
authors.affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Clarke
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Clark
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003062:Codon / Q000235:genetics*; D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D012329:RNA, Bacterial / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012044:Regression Analysis
chemical_list: D003062:Codon; D012329:RNA, Bacterial; D012333:RNA, Messenger