Abstract
The rapid growth in the quantity of available sequence data has made necessary the development of efficient computational tools for its analysis. Substantial progress has been made in the development of tools for the identification and prediction of genes that are expressed via standard decoding. However, since recoded genes embrace only a minority of all genes and since their prediction requires different approaches, they are frequently neglected and as a result are often mis-annotated in the public databases or even left undetected during the annotation process. This chapter aims to describe available computer tools designed for the identification and analysis of recoded genes and public databases that collect information related to recoding. In addition, we also discuss how standard tools for sequence analysis can be used for these purposes.
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Acknowledgments
We are grateful to Drs. Sergi Castellano and Kyungsook Han for careful reading of the manuscript and useful comments. This work was supported by funds from Science Foundation Ireland.
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Firth, A.E., Bekaert, M., Baranov, P.V. (2010). Computational Resources for Studying Recoding. In: Atkins, J., Gesteland, R. (eds) Recoding: Expansion of Decoding Rules Enriches Gene Expression. Nucleic Acids and Molecular Biology, vol 24. Springer, New York, NY. https://doi.org/10.1007/978-0-387-89382-2_20
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