Evaluate the role of the enzymologist in the manual curation and the functional, including metabolic, analysis of genome sequences

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Important (must include) references :
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Thiele, I., & Palsson, B. Ø. (2010). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols, 5(1), 93–121.
Choi, K., & Kim, S. (2008). ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. BMC Bioinformatics, 9, 145.
Caspi, R., Altman, T., Dale, J. M., Dreher, K., Fulcher, C. A., Gilham, F., … Karp, P. D. (2010). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research, 38(Database issue), D473–D479.
Harrow, J., Nagy, A., Reymond, A., Alioto, T., Patthy, L., Antonarakis, S. E., & Guigó, R. (2009). Identifying protein-coding genes in genomic sequences. Genome Biology, 10(1), 201.
Pfeiffer, F., & Oesterhelt, D. (2015). A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes. Life, 5(2), 1427–1444.
Baumgartner, W. A., Cohen, K. B., Fox, L. M., Acquaah-Mensah, G., & Hunter, L. (2007). Manual curation is not sufficient for annotation of genomic databases. Bioinformatics (Oxford, England), 23(13), i41–i48.
Devos, D.; Valencia, A. Intrinsic errors in genome annotation. Trends Genet. 2001, 17, 429–431.
Schnoes, A.M.; Brown, S.D.; Dodevski, I.; Babbitt, P.C. Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol. 2009, 5, e1000605.
Alistair G. Rust, Emmanuel Mongin, Ewan Birney, 2002 Genome annotation techniques: new approaches and challenges, Drug Discovery Today, Volume 7, Issue 11, Pages S70-S76
Mark Yandell1 & Daniel Ence1 A beginner’s guide to eukaryotic genome annotation Nature Reviews Genetics 13, 329-342 (May 2012)

 

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