Nucleic Acids Research Advance Access published online on October 16, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm796
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Database Issue |
eggNOG: automated construction and annotation of orthologous groups of genes
1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2University of Zurich and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland and 3Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strrasse 10, 13092 Berlin, Germany
* To whom correspondence should be addressed. Tel: +49 6221 387 526; Fax: +49 6221 387 517; Email: bork{at}embl.de
Received August 14, 2007. Revised September 14, 2007. Accepted September 17, 2007.
The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes. Here we present the eggNOG database (‘evolutionary genealogy of genes: Non-supervised Orthologous Groups’), which contains orthologous groups constructed from Smith–Waterman alignments through identification of reciprocal best matches and triangular linkage clustering. Applying this procedure to 312 bacterial, 26 archaeal and 35 eukaryotic genomes yielded 43 582 course-grained orthologous groups of which 9724 are extended versions of those from the original COG/KOG database. We also constructed more fine-grained groups for selected subsets of organisms, such as the 19 914 mammalian orthologous groups. We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them. Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.de.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. A. Lee, R. Rentzsch, and C. Orengo GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains Nucleic Acids Res., November 18, 2009; (2009) gkp1049v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Uchiyama, T. Higuchi, and M. Kawai MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity Nucleic Acids Res., November 11, 2009; (2009) gkp948v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. S. Syed, M. D'Antonio, and F. D. Ciccarelli Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes Nucleic Acids Res., November 11, 2009; (2009) gkp957v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Lees, C. Yeats, O. Redfern, A. Clegg, and C. Orengo Gene3D: merging structure and function for a Thousand genomes Nucleic Acids Res., November 11, 2009; (2009) gkp987v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Muller, D. Szklarczyk, P. Julien, I. Letunic, A. Roth, M. Kuhn, S. Powell, C. von Mering, T. Doerks, L. J. Jensen, et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations Nucleic Acids Res., November 9, 2009; (2009) gkp951v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E.V. Koonin, Y.I. Wolf, and P. Puigbo The Phylogenetic Forest and the Quest for the Elusive Tree of Life Cold Spring Harb Symp Quant Biol, August 17, 2009; (2009) sqb.2009.74.006v1. [Abstract] [PDF]
|
|
|
|
|
|
R. S. Datta, C. Meacham, B. Samad, C. Neyer, and K. Sjolander Berkeley PHOG: PhyloFacts orthology group prediction web server Nucleic Acids Res., July 1, 2009; 37(suppl_2): W84 - W89. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. J. Jensen, M. Kuhn, M. Stark, S. Chaffron, C. Creevey, J. Muller, T. Doerks, P. Julien, A. Roth, M. Simonovic, et al. STRING 8--a global view on proteins and their functional interactions in 630 organisms Nucleic Acids Res., January 1, 2009; 37(suppl_1): D412 - D416. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. V. Koonin and Y. I. Wolf Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world Nucleic Acids Res., December 1, 2008; 36(21): 6688 - 6719. [Abstract] [Full Text] [PDF]
|
|