Genome annotation

Genome v/ide correlationa correlation with genome annotation... 

Reboul, J., et al. (2003) C. denims ORFeome version 1.1 experimental verification of the genome annotation and resource for proteome- (, scale protein expression. Nat Genet. 34, 35 1. 

LA Kelley, RM MacCallum, MJE Sternberg. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 299 501-522, 2000. 

Bacillus subtilis SubtiList Institut Pasteur Genome annotation and analysis of bacterium B. subtilis 168 (http //genolist.pasteur. fr/SubtiList/)... 

MicroScope LABGeM—Genoscope Platform for microbial genome annotation and comparative genomics for 640 organisms (https //www.genoscope. cns. fr/age /microscope /home /index.php)... 

K. Eilbeck, S. E. Lewis, C. J. Mungall, M. Yandell, L. Stein, R. Durbin, and M. Ashbumer. 2005. The Sequence Ontology a tool for the unification of genome annotations, Genome Biology, 6 R44. 

Most recently, in silico methods have been apphed to the systems biology of metabolic pathways. An analysis of the human genome assigns 2709 human enzymes to 896 bioreactions 622 of the enzymes are assigned roles in 135 predicted metabolic pathways. The predicted pathways closely match the known nutritional requirements of humans. This analysis identifies probable omissions in the human genome annotation in the form of 203 pathway holes (missing enzymes within the predicted pathways). The predicted human metabolic map is described by a Pathway/Genome Database called HumanCyc, which is available at http //HumanCyc.org/. 

A protein, member of the vitamin K-dependent protein family Genome Annotation Assessment Project http //www.fruitfly.org/GASPl/ ... 

Jarvik, J.W., Fisher, G.W., Shi,C., Hennen, L., Hauser, C., Adler, S. and Berget, P.B. (2002) In vivo functional proteomics Mammalian genome annotation using cd-tagging. BioTechniques 33, 852-867. 

Tebbe, A., Klein, C., Schmidt, A., Bisle, B., Konstandinidis, K., Scheffer, B., Lottspeich, F., Siedler, F., Pfeiffer, F. and Oesterhelt, D. (2005) Analysis of the cytosolic proteome of halobac-terium salinamm - implications for genome annotation and differential expression. Proceedings of the 53rd ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, TX, June5-June9, 2005. 

Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nature Rev. Genet. 2006 7 130-141. 

Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. Systems approach to refining genome annotation. Proc. Natl. Acad. Sci. U.S.A. 2006 103 17480-17484. 

Harbers M, Carninci P. Tag-based approaches for transcriptome research and genome annotation. Nat. Methods 2005 2 495-502. 

There are several ways in which structural genomics has promise as a tool for genome annotation and target prioritization. For genes of unknown function, structure can often provide clues to biochemical function. Sequence homology has become a routine method for functional assignment, but even the most... 

Mao X, Cai T, Olyarchuk JG, Wei L. Automated genome annotation and pathway identification using the KEGG orthology (KO) as a controlled vocabulary. Bioinformatics 2005 21(19) 3787-93. 

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