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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  ...  new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.  ...  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

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  
We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes  ...  The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms.  ...  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

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

C. Dessimoz
2006 Nucleic Acids Research  
We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database.  ...  Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups.  ...  ACKNOWLEDGEMENTS The authors thank G. Cannarozzi, D. Margadant, A. Schneider and two anonymous reviewers for their comments and suggestions on the manuscript.  ... 
doi:10.1093/nar/gkl433 pmid:16835308 pmcid:PMC1500873 fatcat:b4lvrifrbveujajwq4r5wzm33q

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 Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation.  ...  FUTURE DEVELOPMENTS The current updated release of the COGs did not involve creation of new COGs and 242 COGs have been removed from the database.  ... 
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  
, 8.8-, 8.7-, and 4.2-fold, respectively, in terms of sequences, and also considerably increased the number of species.  ...  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-  ...  We used the COG database -used for genome annotation and for studies of phylogenetics and gene evolution -as a model.  ... 
doi:10.4238/vol7-3x-meeting008 fatcat:x5jghohikjg2narjpimdysb5ja

Databases of biological information

M KANEHISA
1998 Trends in Biotechnology  
The new wealth of biological data generated by ongoing genome projects is being used to develop database tools for biologists.This basic biological information can then be interpreted from many viewpoints  ...  -from molecular interactions to interactions among organisms.  ...  database stores the classification of organisms adopted in the GenBank database and the Tree of Life summarizes phylogenetic relationships and the characteristics of organisms.  ... 
doi:10.1016/s0167-7799(98)00133-4 fatcat:r55jacnw2zatffjgxas7hm62xa

Virus Databases ☆ [chapter]

Kathleen McLeod, Chris Upton
2017 Reference Module in Biomedical Sciences  
Acknowledgements The authors would like to thank Chad Smithson for help assembling the collection of virus databases.  ...  This work was supported by a Natural Sciences and Engineering Research Council of Canada Discovery Grant to CU. Conflicts of Interest: The authors are the developers of Virology.ca.  ...  http://bnaber.org/ HIV Broadly Neutralizing Antibodies CAPIH NHRI http://bioinfo-dbb.nhri.org.tw/capih/ Protein interactions for HIV-1 COGs NCBI http://www.ncbi.nlm.nih.gov/COG/ Phylogenetic classification  ... 
doi:10.1016/b978-0-12-801238-3.95728-3 fatcat:hmkdfmz4urgcdjzgo3jqsohace

The Molecular Biology Database Collection: an online compilation of relevant database resources

A. D. Baxevanis
2000 Nucleic Acids Research  
An emphasis has also been placed on including databases where new value is added to the underlying data by virtue of curation, new data connections, or other innovative approaches.  ...  The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more accessible to biologists.  ...  clusters Comparative Genomics Clusters of Orthologous Groups (COG) http://www.ncbi.nlm.nih.gov/COG Phylogenetic classification of proteins from 21 complete genomes XREFdb http://www.ncbi.nlm.nih.gov  ... 
doi:10.1093/nar/28.1.1 pmid:10592167 pmcid:PMC102497 fatcat:cjbf2vh635duvdmnxfpydzbuea

Funybase: a Fungal phylogenomic database

Sylvain Marthey, Gabriela Aguileta, Francois Rodolphe, Annie Gendrault, Tatiana Giraud, Elisabeth Fournier, Manuela Lopez-Villavicencio, Angelique Gautier, Marc-Henri Lebrun, Helene Chiapello
2008 BMC Bioinformatics  
The current release of FUNYBASE contains two types of protein data: (i) a complete set of protein sequences extracted from 30 public fungal genomes and classified into clusters of orthologs using a robust  ...  Description: FUNYBASE is a database dedicated to the analysis of fungal single-copy genes extracted from available fungal genomes sequences, their classification into reliable clusters of orthologs, and  ...  Acknowledgements This study was funded by the French Bureau des Ressources Génétiques (BRG 2005(BRG -2008, an "ANR Blanc" (ANR-06-BLAN-0201) and an "ANR Biodiversity" (ANR-07-BDIV-003). G.  ... 
doi:10.1186/1471-2105-9-456 pmid:18954438 pmcid:PMC2600828 fatcat:vedb7iomvrcyfcsflkfvhswnlq

The iProClass integrated database for protein functional analysis

Cathy H Wu, Hongzhan Huang, Anastasia Nikolskaya, Zhangzhi Hu, Winona C Barker
2004 Computational biology and chemistry  
In particular, the database is organized with PIRSF family classification and maps to other family, function, and structure classification schemes.  ...  Meanwhile, new bioinformatics methods have been developed for inferring protein function using associative analysis of functional properties to complement the traditional sequence homology-based methods  ...  Acknowledgements The project is supported by grant DBI-0138188 from National Science Foundation and grant U01-HG02712 from National Institutes of Health.  ... 
doi:10.1016/j.compbiolchem.2003.10.003 pmid:15022647 fatcat:kkzflwqewfablaw4y2vkmxvzzm

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

A. D. Baxevanis
2001 Nucleic Acids Research  
The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches.  ...  As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research.  ...  Groups (COG) http://www.ncbi.nlm.nih.gov/COG/ Phylogenetic classification of proteins from 21 complete genomes XREFdb http://www.ncbi.nlm.nih.gov/XREFdb/ Cross-referencing of model organism genetics  ... 
doi:10.1093/nar/29.1.1 pmid:11125037 pmcid:PMC29860 fatcat:t7pctxvehncsfliq6a4nywqx5u

IMG: the integrated microbial genomes database and comparative analysis system

V. M. Markowitz, I.-M. A. Chen, K. Palaniappan, K. Chu, E. Szeto, Y. Grechkin, A. Ratner, B. Jacob, J. Huang, P. Williams, M. Huntemann, I. Anderson (+3 others)
2011 Nucleic Acids Research  
IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses.  ...  IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context.  ...  ACKNOWLEDGEMENTS We thank Henrik Nordberg, Roman Nikitin, Simon Minovitsky, Amrita Pati, Konstantinos Liolios and Ioanna Pagani for their contribution to the development and maintenance of IMG.  ... 
doi:10.1093/nar/gkr1044 pmid:22194640 pmcid:PMC3245086 fatcat:5kywy2f2ezf37f5scio42kptgy

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  ...  The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most recently, in 2014  ...  patterns of presence-absence of (proteins from) the compared genomes in a given COG that facilitate functional annotation of new genomes and evolutionary inference.  ... 
doi:10.1093/nar/gkaa1018 pmid:33167031 fatcat:4c77x5ponfht5im2v4pu76byli

MBGD: microbial genome database for comparative analysis

I. Uchiyama
2003 Nucleic Acids Research  
The created classification table is stored into the database and can be explored combining with the data of individual genomes as well as similarity relationships among genomes.  ...  The central function of MBGD is to create an orthologous gene classification table using precomputed all-against-all similarity relationships among genes in multiple genomes.  ...  This work was supported in part by Grant-in-Aid for Scientific Researches on Priority Areas (C) 'Genome Information Science' from Ministry of Education, Culture, Sports, Science and Technology of Japan  ... 
doi:10.1093/nar/gkg109 pmid:12519947 pmcid:PMC165556 fatcat:ele6faew25ehhczlxlnezilzmu

Improving Microbial Genome Annotations in an Integrated Database Context

I-Min A. Chen, Victor M. Markowitz, Ken Chu, Iain Anderson, Konstantinos Mavromatis, Nikos C. Kyrpides, Natalia N. Ivanova, John Parkinson
2013 PLoS ONE  
We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems  ...  Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes.  ...  development and maintenance of the IMG systems.  ... 
doi:10.1371/journal.pone.0054859 pmid:23424620 pmcid:PMC3570495 fatcat:bio2te2hhvhjzfxufl5ej2exoi
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