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The identification of pseudogenes is an integral and significant part of the genome annotation because of their abundance and their impact on the experimental analysis of functional genes. Most of the computational annotation systems are not optimized for systematic pseudogene recognition, often annotating pseudogenes as functional genes, and users then propagate these errors to subsequent analyses and interpretations.
(Yao et al., 2006) Systematic identification of pseudogenes through whole genome expression evidence profiling. Nucleic Acids Res.