PMID:15347574

Citation	Firth, AE and Brown, CM (2005) Detecting overlapping coding sequences with pairwise alignments. Bioinformatics 21:282-92
Abstract	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.
Links	PubMed Online version:10.1093/bioinformatics/bti007
Keywords	Algorithms; Computer Simulation; Conserved Sequence; DNA Mutational Analysis/methods; Genes, Overlapping/genetics; Models, Genetic; Models, Statistical; Open Reading Frames/genetics; Sequence Alignment/methods; Sequence Analysis, DNA/methods; Sequence Homology, Nucleic Acid
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