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The COG database: an updated version includes eukaryotes

Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov (+5 others)
2003 BMC Bioinformatics  
The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes  ...  Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result  ...  Aravind, David Lipman, Kira Makarova and Wei Yang for useful discussions, and Igor Garkavtsev for his contributions at the initial stages of the KOG project.  ... 
doi:10.1186/1471-2105-4-41 pmid:12969510 pmcid:PMC222959 fatcat:xuukptdqqnf3bfyb6zpg2gsdfi

The COG database: new developments in phylogenetic classification of proteins from complete genomes

R. L. Tatusov
2001 Nucleic Acids Research  
The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs  ...  The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit  ...  ACKNOWLEDGEMENTS The authors are grateful to David Lipman for his critical contribution at the initial stage of the COG project and constant support and inspiration and to Vivek Anantharaman, L.  ... 
doi:10.1093/nar/29.1.22 pmid:11125040 pmcid:PMC29819 fatcat:ary2byy25vhavdoqrxn4kd365i

Expanded microbial genome coverage and improved protein family annotation in the COG database

Michael Y. Galperin, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin
2014 Nucleic Acids Research  
Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all  ...  The new version of the COGs is expected to become an important tool for microbial genomics.  ...  CHANGES IN THE COG DATABASE Compared to the previous versions of the COG database, the current release provides substantially expanded genome coverage and updated annotation of the COGs.  ... 
doi:10.1093/nar/gku1223 pmid:25428365 pmcid:PMC4383993 fatcat:kpj2jbme2va5dlq3bbq5uq7p5y

A procedure to recruit members to enlarge protein family databases - the building of UECOG (UniRef-Enriched COG Database) as a model

G.R. Fernandes, D.V.C. Barbosa, F. Prosdocimi, I.A. Pena, L. Santana-Santos, O. Coelho Junior, A. Barbosa-Silva, H.M. Velloso, M.A. Mudado, D.A. Natale, A.C. Faria-Campos, S.C.V. Aguiar (+1 others)
2008 Genetics and Molecular Research  
Presently, the UniRef50-based recruitment procedure enriches the COG database for Archaea, Bacteria and its subgroups Actinobacteria, Firmicutes, Proteobacteria, and other bacteria by 2. 2-, 8.0-, 7.0-  ...  content, and neighbor-joining single-linkage, and observed that the former four agree in their validations.  ...  Production of an updated version of COG COG is the most used ortholog database for genome and gene annotation analyses. It was initially built in 1997 and further updated in 2001.  ... 
doi:10.4238/vol7-3x-meeting008 fatcat:x5jghohikjg2narjpimdysb5ja

Overview and comparison of ortholog databases

Andrey Alexeyenko, Julia Lindberg, Åsa Pérez-Bercoff, Erik L.L. Sonnhammer
2006 Drug Discovery Today : Technologies  
The goal of this review is to compare their contents and clarify which database is most suited for a certain task.  ...  Orthologs are an indispensable bridge to transfer biological knowledge between species, from protein annotations to sophisticated disease models. However, orthology assignment is not trivial.  ...  The latest version of the InParanoid database contains 21 eukaryotic organisms plus Escherichia coli.  ... 
doi:10.1016/j.ddtec.2006.06.002 pmid:24980400 fatcat:2rw37btp4nfthavz3zsjlcp3mq

The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection

Michael Y. Galperin, Daniel J. Rigden, Xosé M. Fernández-Suárez
2015 Nucleic Acids Research  
The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously  ...  This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets.  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their help in compiling this issue.  ... 
doi:10.1093/nar/gku1241 pmid:25593347 pmcid:PMC4383995 fatcat:rpqeohyapre5rijy7vfn7r2p7a

Database resources of the National Center for Biotechnology

D. L. Wheeler
2003 Nucleic Acids Research  
The COGs are now also linked to the proteins of two higher eukaryotes; C. elegans and D. melanogaster.  ...  The human version of the Map Viewer is tightly integrated with other NCBI databases such as LocusLink and dbSNP.  ... 
doi:10.1093/nar/gkg033 pmid:12519941 pmcid:PMC165480 fatcat:dydxcilrszbt7g67rljindwu2a

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

R. Zhang, Y. Lin
2009 Nucleic Acids Research  
Five years after we constructed DEG, a database of essential genes, DEG 5.0 has significant advances over the 2004 version in both the number of essential genes and the number of organisms in which these  ...  These updates not only represent significant advances of DEG, but also represent the rapid progress of the essentialgene field. DEG is freely available at the website  ...  ACKNOWLEDGEMENTS We would like to thank the anonymous referees for their constructive comments.  ... 
doi:10.1093/nar/gkn858 pmid:18974178 pmcid:PMC2686491 fatcat:2xuqt67qyrfgpbajn7latmu2hu

The Molecular Biology Database Collection: an updated compilation of biological database resources

A. D. Baxevanis
2001 Nucleic Acids Research  
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community.  ...  Short, searchable summaries of each of the databases included in the Collection are available through the Nucleic Acids Research Web site, at http://www.nar.oupjournals.org.  ...  These reviewed databases are collectively listed in the Molecular Biology Database Collection. The databases included in the current version of the Collection are shown in Table 1 .  ... 
doi:10.1093/nar/29.1.1 pmid:11125037 pmcid:PMC29860 fatcat:t7pctxvehncsfliq6a4nywqx5u

GoSynthetic database tool to analyse natural and engineered molecular processes

Chunguang Liang, Beate Krüger, Thomas Dandekar
2013 Database: The Journal of Biological Databases and Curation  
The current version of GoSynthetic covers more than one million processes, proteins, COGs and GOs.  ...  Furthermore, protein interaction data, cross-links to organism-specific databases (17 organisms including six model organisms and their interactions), COG/KOG, GO and IntAct are warehoused.  ...  The database is regularly updated. Protein identifiers from organism-specific databases (latest versions) are merged into each updated GoSynthetic database.  ... 
doi:10.1093/database/bat043 pmid:23813641 pmcid:PMC3694605 fatcat:keiz7nqbqncgtd4ev56uvo2a7u

The PEDANT genome database

D. Frishman
2003 Nucleic Acids Research  
OVERVIEW AND STATUS OF THE PEDANT DATABASE IN 2003 When the first version of the PEDANT genome database was launched in 1996 (1) it provided a computational analysis of the five first completely sequenced  ...  In the past seven years, the PEDANT genome analysis software has matured (2): it is now based on an efficient relational database schema compatible with both MySQL TM and Oracle TM database management  ...  , including all publicly available eukaryotic genomes.  ... 
doi:10.1093/nar/gkg005 pmid:12519983 pmcid:PMC165452 fatcat:iimwfhvp7ncwppddguseu4z7km

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Michael Y Galperin, Yuri I Wolf, Kira S Makarova, Roberto Vera Alvarez, David Landsman, Eugene V Koonin
2020 Nucleic Acids Research  
The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with  ...  In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI's gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or  ...  KEY CHANGES IN THE 2020 COG UPDATE Expanded genome coverage In the current update, the genome coverage of the COG database has been expanded to include representatives of all bacterial and archaeal genera  ... 
doi:10.1093/nar/gkaa1018 pmid:33167031 fatcat:4c77x5ponfht5im2v4pu76byli

Database resources of the National Center for Biotechnology Information: update

D. L. Wheeler
2004 Nucleic Acids Research  
A eukaryotic version, KOGs, is now available for seven eukaryotes including Homo sapiens, C.elegans, Drosophila melanogaster and Arabidopsis thaliana.  ...  All reagents are characterized for allele speci®city using an updated allele database based on IMGT/HLA.  ... 
doi:10.1093/nar/gkh073 pmid:14681353 pmcid:PMC308807 fatcat:s3wdhcgegfexrokvqtbtpvotf4

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2000 Nucleic Acids Research  
The online version of this article has been published under an open access model.  ...  ; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its  ...  A eukaryotic version, KOGs, is available for seven eukaryotes, including H.sapiens, C.elegans, D.melanogaster and A.thaliana.  ... 
doi:10.1093/nar/28.1.10 pmid:10592169 pmcid:PMC102437 fatcat:xhsgpitasrd3na5mmjgz274zcq

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2006 Nucleic Acids Research  
In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by the National Institutes of Health. Conflict of interest statement. None declared.  ...  A eukaryotic version, KOGs, is available for seven organisms including H.sapiens; C.elegans, D.melanogaster and A.thaliana.  ... 
doi:10.1093/nar/gkj158 pmid:16381840 pmcid:PMC1347520 fatcat:ajgh422s6nbi3o4beemsncsyzi
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