The COG database: an updated version includes eukaryotes
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* Corresponding author: Roman L Tatusov tatusov@ncbi.nlm.nih.gov
BMC Bioinformatics 2003, 4:41 doi:10.1186/1471-2105-4-41
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Data Note
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Review
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Correspondence
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Methodology article
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Software
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Research
Igor B Rogozin, Karen Thomson, Miklós Csürös, Liran Carmel, Eugene V Koonin Biology Direct 2008, 3:7 (17 March 2008) Homoplasy denotes the same (parallel) mutations occurring independently in different lineages. It is a scourge of phylogenetic methods. Here, however, it is shown that homoplasy is also an interesting evolutionary phenomenon. Homplasy seems, at least, in part, to underlie the so-called homologous series of phenotypic variation occurring in different, particularly, closely related lineages, an effect first described by the famous Russian geneticict Vavilov some 90 years ago.
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Software
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Research
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Proceedings
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Method
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Research
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Database
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Research
The distributions, mechanisms, and structures of metabolite-binding riboswitches Jeffrey E Barrick, Ronald R Breaker Genome Biology 2007, 8:R239 (12 November 2007) Phylogenetic analyses revealed insights into the distribution of riboswitch classes in different microbial groups, and structural analyses led to updated aptamer structure models and insights into the mechanism of these non-coding RNA structures. |
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Research article
Poly-G/poly-C tracts in the genomes of Caenorhabditis Yang Zhao, Nigel J O'Neil, Ann M Rose BMC Genomics 2007, 8:403 (7 November 2007) |
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Database
CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks Jan Baumbach BMC Bioinformatics 2007, 8:429 (6 November 2007) |
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Proceedings
Towards validating the hypothesis of phylogenetic profiling Raja Loganantharaj, Mazen Atwi BMC Bioinformatics 2007, 8(Suppl 7):S25 (1 November 2007) |
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Research article
Dennis R Livesay, Patrick D Kidd, Sepehr Eskandari, Usman Roshan BMC Bioinformatics 2007, 8:397 (17 October 2007) |
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Research article
Tobias Wittkop, Jan Baumbach, Francisco P Lobo, Sven Rahmann BMC Bioinformatics 2007, 8:396 (17 October 2007) |
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Research article
Manuel Irimia, Jakob Rukov, David Penny, Scott Roy BMC Evolutionary Biology 2007, 7:188 (4 October 2007) |
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Research article
Jesper Larsen, Peter Kuhnert, Joachim Frey, Henrik Christensen, Magne Bisgaard, John E Olsen BMC Evolutionary Biology 2007, 7:184 (3 October 2007) |
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Research article
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties Jos Boekhorst, Berend Snel BMC Bioinformatics 2007, 8:356 (21 September 2007) Using basic gene properties like gene length and gene order dramatically improves the division of results in the BLAST 'gray zone' into spurious matches and genuine hits.
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Research article
Uncovering the mutation-fixation correlation in short lineages Eric J Vallender, Bruce T Lahn BMC Evolutionary Biology 2007, 7:168 (21 September 2007) |
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Research
Fabrizio Lillo, David C Krakauer Biology Direct 2007, 2:22 (18 September 2007) |
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Research article
Diego Miranda-Saavedra, Michael JR Stark, Jeremy C Packer, Christian P Vivares, Christian Doerig, Geoffrey J Barton BMC Genomics 2007, 8:309 (4 September 2007) |
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Research article
Global analysis of host response to induction of a latent bacteriophage Robin E Osterhout, Israel A Figueroa, Jay D Keasling, Adam P Arkin BMC Microbiology 2007, 7:82 (31 August 2007) |
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Research article
Eiko E Kuramae, Vincent Robert, Carlos Echavarri-Erasun, Teun Boekhout BMC Evolutionary Biology 2007, 7:134 (9 August 2007) |
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Method
Novel metrics for evaluating the functional coherence of protein groups via protein semantic network Bin Zheng, Xinghua Lu Genome Biology 2007, 8:R153 (31 July 2007) Metrics are presented for assessing overall functional coherence of a group of proteins based on the associated biomedical literature. |
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Software
PHIDIAS: a pathogen-host interaction data integration and analysis system Zuoshuang Xiang, Yuying Tian, Yongqun He Genome Biology 2007, 8:R150 (30 July 2007) PHIDIAS is a web-based database system serving as a centralized source to search, compare and analyse integrated genome sequences, conserved domains and transcriptional data related to pathogen-host interactions. |
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Research article
Identification of gene targets against dormant phase Mycobacterium tuberculosis infections Dennis J Murphy, James R Brown BMC Infectious Diseases 2007, 7:84 (26 July 2007) |
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Database
TrED: the Trichophyton rubrum Expression Database Jian Yang, Lihong Chen, Lingling Wang, Wenliang Zhang, Tao Liu, Qi Jin BMC Genomics 2007, 8:250 (25 July 2007) |
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Research
Yoshitoshi Ogura, Tadasuke Ooka, Asadulghani, Jun Terajima, Jean-Philippe Nougayrède, Ken Kurokawa, Kousuke Tashiro, Toru Tobe, Keisuke Nakayama, Satoru Kuhara, Eric Oswald, Haruo Watanabe, Tetsuya Hayashi Genome Biology 2007, 8:R138 (10 July 2007) Comparing the genomes of O157 and non-O157 enterohemorrhagic |
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Research
Stephen E Von Stetina, Joseph D Watson, Rebecca M Fox, Kellen L Olszewski, W Clay Spencer, Peter J Roy, David M Miller Genome Biology 2007, 8:R135 (5 July 2007) A novel strategy for profiling |
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Software
Namshin Kim, Christopher Lee BMC Bioinformatics 2007, 8:213 (20 June 2007) |
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Research article
Elisabeth F Schwartz, Elia Diego-Garcia, Ricardo C Rodríguez de la Vega, Lourival D Possani BMC Genomics 2007, 8:119 (16 May 2007) |
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Research article
Structural and functional insights into Mimivirus ORFans Harpreet Saini, Daniel Fischer BMC Genomics 2007, 8:115 (9 May 2007) |
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Research article
An insight into the sialome of the oriental rat flea, Xenopsylla cheopis (Rots) John F Andersen, B Joseph Hinnebusch, David A Lucas, Thomas P Conrads, Timothy D Veenstra, Van M Pham, José MC Ribeiro BMC Genomics 2007, 8:102 (16 April 2007) |
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Research article
Modelling the evolution of the archaeal tryptophan synthase Rainer Merkl BMC Evolutionary Biology 2007, 7:59 (10 April 2007) |
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Methodology article
Orthology prediction at scalable resolution by phylogenetic tree analysis René TJM van der Heijden, Berend Snel, Vera van Noort, Martijn A Huynen BMC Bioinformatics 2007, 8:83 (8 March 2007) |
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Research article
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases Karolina L Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Janusz M Bujnicki BMC Bioinformatics 2007, 8:73 (5 March 2007) |
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Research
Genome display tool: visualizing features in complex data sets Lalitha Viswanath, Yue Lu, George E Fox Source Code for Biology and Medicine 2007, 2:1 (14 February 2007) |
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Research
Phylogenetic signal and functional categories in Proteobacteria genomes Iñaki Comas, Andrés Moya, Fernando González-Candelas BMC Evolutionary Biology 2007, 7(Suppl 1):S7 (8 February 2007) |
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Research
Wei-Jen Chang, Victoria M Addis, Anya J Li, Elin Axelsson, David H Ardell, Laura F Landweber Biology Direct 2007, 2:6 (1 February 2007) |
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Method
Prediction of effective genome size in metagenomic samples Jeroen Raes, Jan O Korbel, Martin J Lercher, Christian von Mering, Peer Bork Genome Biology 2007, 8:R10 (15 January 2007) A novel computational approach shows a link between genome size and habitat from analysis of environmental metagenomic DNA reads. |
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Method
John Wang, Stephanie Jemielity, Paolo Uva, Yannick Wurm, Johannes Gräff, Laurent Keller Genome Biology 2007, 8:R9 (15 January 2007) An annotated EST resource for the fire ant Solenopsis invicta containing 21,715 ESTs, which represent 11,864 putatively different transcripts, and a corresponding cDNA microarray are described. |
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Software
DiscoverySpace: an interactive data analysis application Neil Robertson, Mehrdad Oveisi-Fordorei, Scott D Zuyderduyn, Richard J Varhol, Christopher Fjell, Marco Marra, Steven Jones, Asim Siddiqui Genome Biology 2007, 8:R6 (8 January 2007) DiscoverySpace, a graphical application for bioinformatics data analysis, in particular analysis of SAGE data, is described |
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Research article
An annotated catalogue of salivary gland transcripts in the adult female mosquito, Ædes ægypti* José MC Ribeiro, Bruno Arcà, Fabrizio Lombardo, Eric Calvo, Van My Phan, Prafulla K Chandra, Stephen K Wikel BMC Genomics 2007, 8:6 (4 January 2007) |
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Research
Evolutionary conservation of domain-domain interactions Zohar Itzhaki, Eyal Akiva, Yael Altuvia, Hanah Margalit Genome Biology 2006, 7:R125 (21 December 2006) Mapping of domain-domain interactions onto the cellular protein-protein interaction networks of different organisms demonstrates that there is a catalogue of domain pairs that is used for mediating various interactions in the cell |
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Comment
Did the last common ancestor have a biological membrane? Gáspár Jékely Biology Direct 2006, 1:35 (27 November 2006) |
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Review
Lyn-Marie Birkholtz, Olivier Bastien, Gordon Wells, Delphine Grando, Fourie Joubert, Vinod Kasam, Marc Zimmermann, Philippe Ortet, Nicolas Jacq, Nadia Saïdani, Sylvaine Roy, Martin Hofmann-Apitius, Vincent Breton, Abraham I Louw, Eric Maréchal Malaria Journal 2006, 5:110 (17 November 2006) A review of the different tools and strategies that have recently been developed to process the huge amount of data produced by the X-omic projects. This includes the comparison of protein sequences, high throughput reconstruction of molecular phylogenies, representation of biological processes, methods to integrate X-omic generated data following drug treatments and in silico prediction of protein structure and identification of specific ligand.
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Research article
Hong-Liang Yang, Yong-Zhang Zhu, Jin-Hong Qin, Ping He, Xu-Cheng Jiang, Guo-Ping Zhao, Xiao-Kui Guo BMC Genomics 2006, 7:293 (16 November 2006) |
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Methodology article
Integration of curated databases to identify genotype-phenotype associations Chern-Sing Goh, Tara A Gianoulis, Yang Liu, Jianrong Li, Alberto Paccanaro, Yves A Lussier, Mark Gerstein BMC Genomics 2006, 7:257 (12 October 2006) |
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Research article
Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags Lingling Wang, Li Ma, Wenchuan Leng, Tao Liu, Lu Yu, Jian Yang, Li Yang, Wenliang Zhang, Qian Zhang, Jie Dong, Ying Xue, Yafang Zhu, Xingye Xu, Zhe Wan, Guohui Ding, Fudong Yu, Kang Tu, Yixue Li, Ruoyu Li, Yan Shen, Qi Jin BMC Genomics 2006, 7:255 (11 October 2006) |
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Software
Todd J Treangen, Xavier Messeguer BMC Bioinformatics 2006, 7:433 (5 October 2006) |
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Research article
Comparative assessment of performance and genome dependence among phylogenetic profiling methods Evan S Snitkin, Adam M Gustafson, Joseph Mellor, Jie Wu, Charles DeLisi BMC Bioinformatics 2006, 7:420 (27 September 2006) |
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Hypothesis
Pavel V Baranov, Bente Vestergaard, Thomas Hamelryck, Raymond F Gesteland, Jens Nyborg, John F Atkins Biology Direct 2006, 1:28 (13 September 2006) |
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Research article
Olaf Brockmann-Gretza, Jörn Kalinowski BMC Genomics 2006, 7:230 (8 September 2006) |
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Research article
Daniel H Haft, Ian T Paulsen, Naomi Ward, Jeremy D Selengut BMC Biology 2006, 4:29 (24 August 2006) A conserved C-terminal domain distributed across bacterial species found in sediment, soil and biofilms, identified using a rapid phylogenetic profiling method, appears to be involved in protein export sorting in exopolysaccharide production.
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Research article
Yanbin Yin, Daniel Fischer BMC Evolutionary Biology 2006, 6:63 (16 August 2006) |
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Research article
Cross genome comparisons of serine proteases in Arabidopsis and rice Lokesh P Tripathi, R Sowdhamini BMC Genomics 2006, 7:200 (9 August 2006) |
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Research
Diana Ekman, Sara Light, Åsa K Björklund, Arne Elofsson Genome Biology 2006, 7:R45 (16 June 2006) An analysis of hubs (proteins with many interactors) and non-hubs in the S. cerevisiae protein interaction network shows that hub proteins are enriched with multiple and repeated domains.
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Research article
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga G Troyanskya, Trey Ideker, Kara Dolinski, Nizar N Batada, Mike Tyers Journal of Biology 2006, 5:11 (8 June 2006) A new literature-based yeast database documents over 33,000 biological interactions, manually curated from the primary literature, and provides an invaluable resource to benchmark high-throughput methods in the study of complex networks.
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Methodology article
David J Reiss, Nitin S Baliga, Richard Bonneau BMC Bioinformatics 2006, 7:280 (2 June 2006) |
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Research
Similarity searches in genome-wide numerical data sets Galina Glazko, Michael Coleman, Arcady Mushegian Biology Direct 2006, 1:13 (30 May 2006) |
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Methodology article
Improving the specificity of high-throughput ortholog prediction Debra L Fulton, Yvonne Y Li, Matthew R Laird, Benjamin GS Horsman, Fiona M Roche, Fiona SL Brinkman BMC Bioinformatics 2006, 7:270 (28 May 2006) A new high-throughput method, Ortholuge, utilizes phylogenetic distance ratios to distinguish orthologous genes from those that are paralogous, and can be used on bacteria and eukaryotes on a genome-wide scale.
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Research article
Phylogenomic analysis of the GIY-YIG nuclease superfamily Stanislaw Dunin-Horkawicz, Marcin Feder, Janusz M Bujnicki BMC Genomics 2006, 7:98 (28 April 2006) |
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Research
Benchmarking ortholog identification methods using functional genomics data Tim Hulsen, Martijn A Huynen, Jacob de Vlieg, Peter MA Groenen Genome Biology 2006, 7:R31 (13 April 2006) A benchmarking of the most popular orthologous identification methods using functional genomics data identifies the two best methods. |
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Database
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database Paramvir S Dehal, Jeffrey L Boore BMC Bioinformatics 2006, 7:201 (11 April 2006) |
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Research article
Ruslan I Sadreyev, Nick V Grishin BMC Structural Biology 2006, 6:6 (20 March 2006) |
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Database
Domain-based small molecule binding site annotation Kevin A Snyder, Howard J Feldman, Michel Dumontier, John J Salama, Christopher WV Hogue BMC Bioinformatics 2006, 7:152 (17 March 2006) |
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Research
Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf, Eugene V Koonin Biology Direct 2006, 1:7 (16 March 2006) Computational analysis shows that CRISPR repeats and associated Cas proteins in prokaryotes might act in conjunction as a RNA-silencing mechanism against plasmids and viruses, similar to the eukaryotic RNA-interference system.
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Methodology article
Gene annotation and network inference by phylogenetic profiling Jie Wu, Zhenjun Hu, Charles DeLisi BMC Bioinformatics 2006, 7:80 (17 February 2006) |
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Method
Predicting genes for orphan metabolic activities using phylogenetic profiles Lifeng Chen, Dennis Vitkup Genome Biology 2006, 7:R17 (15 February 2006) A method that combines local structure of a metabolic network with phylogenetic profiles is described and used to assign genes to orphan metabolic activities in yeast and |
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Research article
Andreas Simon, Gernot Glöckner, Marius Felder, Michael Melkonian, Burkhard Becker BMC Plant Biology 2006, 6:2 (13 February 2006) According to EST comparisons, the scaly flagellate green alga, Mesostigma viride, shares more genes with embryophytes than with Chlamydomonas and may be a unicellular model for the last flagellate common ancestor of the streptophytes.
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Research article
Karolina L Tkaczuk, Agnieszka Obarska, Janusz M Bujnicki BMC Evolutionary Biology 2006, 6:6 (24 January 2006) Phylogenetic and fold-recognition analysis of homologs of HEN1, a key enzyme in plant microRNA biogenesis, yields a structural model of the catalytic domain and reveals HEN1 to be related to small-molecule methyltransferases.
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Methodology article
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs Bradford C Powell, Clyde A Hutchison BMC Bioinformatics 2006, 7:31 (19 January 2006) |
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Research article
Etienne GJ Danchin, Philippe Gouret, Pierre Pontarotti BMC Evolutionary Biology 2006, 6:5 (18 January 2006) The absence of certain gene families that are conserved throughout other eukaryotes suggests that the human genome, which is generally considered to have evolved to high levels of complexity, has also undergone simplification and specific gene loss.
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Research article
Peter Gaudermann, Ina Vogl, Evelyn Zientz, Francisco J Silva, Andres Moya, Roy Gross, Thomas Dandekar BMC Microbiology 2006, 6:1 (9 January 2006) Reannotation of the Blochmannia floridanus genome using data from related species expands the knowledge of the symbiont's metabolic repertoire and highlights many conserved proteobacterial proteins.
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Software
Ulysses - an application for the projection of molecular interactions across species Danielle Kemmer, Yong Huang, Sohrab P Shah, Jonathan Lim, Jochen Brumm, Macaire MS Yuen, John Ling, Tao Xu, Wyeth W Wasserman, BF Francis Ouellette Genome Biology 2005, 6:R106 (2 December 2005) Ulysses, a new software for the parallel analysis and display of protein interactions detected in various species, is described. |
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Research article
Natural history of S-adenosylmethionine-binding proteins Piotr Z Kozbial, Arcady R Mushegian BMC Structural Biology 2005, 5:19 (14 October 2005) Analysis of the phyletic distribution and structural similarities of S-adenosylmethionine-binding proteins indicate that two widespread folds, the Rossman fold and TIM barrel, have repeatedly evolved for diverse types of reactions that require S-adenosylmethionine.
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Software
Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis François Enault, Karsten Suhre, Jean-Michel Claverie BMC Bioinformatics 2005, 6:247 (12 October 2005) Gene Function Predictor, included in the updated Phydbac tool compares well with other genomic context servers in proposing putative associations between Escherichia coli K-12 proteins, demonstrating an accuracy of over 70% in the linkage of these predictions to gene ontology terms.
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Research article
Emmanuel G Reynaud, Miguel A Andrade, Fabien Bonneau, Thi Ly, Michael Knop, Klaus Scheffzek, Rainer Pepperkok BMC Biology 2005, 3:21 (7 October 2005) The expansion of a unique family of essential circularly permuted GTPases related to the human Lsg1 correlates with the evolution of compartmentalization of eukaryotic cells.
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Research article
Soumyadeep Nandi, Nipun Mehra, Andrew M Lynn, Alok Bhattacharya BMC Genomics 2005, 6:116 (9 September 2005) |
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Research article
Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa Marcus Bräutigam, Angelica Lindlöf, Shakhira Zakhrabekova, Gokarna Gharti-Chhetri, Björn Olsson, Olof Olsson BMC Plant Biology 2005, 5:18 (1 September 2005) |
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Methodology article
Peter Sperisen, Marco Pagni BMC Bioinformatics 2005, 6:216 (31 August 2005) |
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Research
Keith A Corbino, Jeffrey E Barrick, Jinsoo Lim, Rüdiger Welz, Brian J Tucker, Izabela Puskarz, Maumita Mandal, Noam D Rudnick, Ronald R Breaker Genome Biology 2005, 6:R70 (1 August 2005) Comparative sequence analysis and structural probing identified five RNA elements in the intergenic region of |
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Proceedings
H Fang, W Tong, R Perkins, L Shi, H Hong, X Cao, Q Xie, SH Yim, JM Ward, HC Pitot, YP Dragan BMC Bioinformatics 2005, 6(Suppl 2):S6 (15 July 2005) |
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Research article
Jan Kosinski, Marcin Feder, Janusz M Bujnicki BMC Bioinformatics 2005, 6:172 (12 July 2005) New members of the PD-(D/E)XK superfamily, with potential nuclease activity, have been identified using HHsearch, a combined sequence/structure method for the detection of remote homology.
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Software
AutoFACT: An Automatic Functional Annotation and Classification Tool Liisa B Koski, Michael W Gray, B Franz Lang, Gertraud Burger BMC Bioinformatics 2005, 6:151 (16 June 2005) |
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Research article
Michael Y Galperin BMC Microbiology 2005, 5:35 (14 June 2005) A comprehensive census of bacterial and archaeal signal transduction sequences reveals that the complexity of signalling systems can generally be correlated with the phylogenetic position and lifestyle of the organism, and that Wolinella succinogenes has the highest 'IQ' as measured by the number of encoded signal transducers.
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Software
Predicting functional sites with an automated algorithm suitable for heterogeneous datasets David La, Dennis R Livesay BMC Bioinformatics 2005, 6:116 (13 May 2005) |
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Software
ProGenExpress: Visualization of quantitative data on prokaryotic genomes Michael Watson BMC Bioinformatics 2005, 6:98 (13 April 2005) |
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Research article
Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold Michael Roßbach, Oliver Daumke, Claudia Klinger, Alfred Wittinghofer, Michael Kaufmann BMC Structural Biology 2005, 5:7 (20 March 2005) |
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Research article
Adriana Ravagnani, Christopher L Finan, Michael Young BMC Genomics 2005, 6:39 (17 March 2005) |
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Research article
A comprehensive update of the sequence and structure classification of kinases Sara Cheek, Krzysztof Ginalski, Hong Zhang, Nick V Grishin BMC Structural Biology 2005, 5:6 (16 March 2005) An updated classification of the almost 60,000 known kinases allows a comprehensive structural annotation of all 25 subfamilies and provides a strong basis on which to classify any newly discovered family members.
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Research
Rowena E Martin, Roselani I Henry, Janice L Abbey, John D Clements, Kiaran Kirk Genome Biology 2005, 6:R26 (2 March 2005) Bioinformatic and expression analyses attribute putative functions to transporters and channels encoded by the |
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Research article
Marcin Feder, Janusz M Bujnicki BMC Genomics 2005, 6:21 (18 February 2005) |
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Software
GenomeViz: visualizing microbial genomes Rohit Ghai, Torsten Hain, Trinad Chakraborty BMC Bioinformatics 2004, 5:198 (15 December 2004) |
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Software
Florian Meereis, Michael Kaufmann BMC Bioinformatics 2004, 5:150 (15 October 2004) |
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Research article
Duplicated genes evolve slower than singletons despite the initial rate increase I King Jordan, Yuri I Wolf, Eugene V Koonin BMC Evolutionary Biology 2004, 4:22 (6 July 2004) Following gene duplication there is a period of rapid evolution, which then slows down in cases where the original gene has an important biological function and the duplicate is retained.
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Research
Galina V Glazko, Arcady R Mushegian Genome Biology 2004, 5:R32 (27 April 2004) A hierarchy of 3,688 phyletic patterns was characterized encompassing more than 5,000 known protein-coding genes from 66 complete microbial genomes. The results indicate that gene loss and displacement has occurred in the evolution of most pathways. |
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Research
The regulatory content of intergenic DNA shapes genome architecture Craig E Nelson, Bradley M Hersh, Sean B Carroll Genome Biology 2004, 5:R25 (15 March 2004) The relationship between regulatory complexity and gene spacing was examined in |
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Research
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale Genome Biology 2004, 5:R7 (15 January 2004) We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes. |