title: Detecting overlapping coding sequences with pairwise alignments.
abstract: BACKGROUND
  Overlapping gene coding sequences (CDSs) are particularly common in viruses but also occur in more complex genomes. Detecting such genes with conventional gene-finding algorithms can be difficult for several reasons. If an overlapping CDS is on the same read-strand as a known CDS, then there may not be a distinct promoter or mRNA. Furthermore, the constraints imposed by double-coding can result in atypical codon biases. However, these same constraints lead to particular mutation patterns that may be detectable in sequence alignments.
  
  
  RESULTS
  In this paper, we investigate several statistics for detecting double-coding sequences with pairwise alignments--including a new maximum-likelihood method. We also develop a model for double-coding sequence evolution. Using simulated sequences generated with the model, we characterize the distribution of each statistic as a function of sequence composition, length, divergence time and double-coding frame. Using these results, we develop several algorithms for detecting overlapping CDSs. The algorithms were tested on known overlapping CDSs and other overlapping open reading frames (ORFs) in the hepatitis B virus (HBV), Escherichia coli and Salmonella typhimurium genomes. The algorithms should prove useful for detecting novel overlapping genes--especially short coding ORFs in viruses.
  
  
  BACKGROUND
  Programs may be obtained from the authors.
  
  
  BACKGROUND
  http://biochem.otago.ac.nz/double.html.
authors.affiliation: Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Firth
authors.forename: Chris M
authors.initials: CM
authors.lastname: Brown
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D017124:Conserved Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D005807:Genes, Overlapping / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D016366:Open Reading Frames / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid