Detecting overlapping coding sequences in virus genomes |
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Authors: | Andrew E Firth and Chris M Brown |
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Affiliation: | (1) Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand |
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Abstract: | Background Detecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret – especially within overlapping genes; and viruses often employ non-canonical translational mechanisms – e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites – which can conceal potentially coding open reading frames (ORFs). |
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