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The COG database: new developments in phylogenetic classification of proteins from complete genomes
2001
Nucleic Acids Research
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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
2003
BMC Bioinformatics
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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
2006
Nucleic Acids Research
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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
2014
Nucleic Acids Research
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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
2008
Genetics and Molecular Research
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, 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
1998
Trends in Biotechnology
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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]
2017
Reference Module in Biomedical Sciences
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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
2000
Nucleic Acids Research
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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
2008
BMC Bioinformatics
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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
2004
Computational biology and chemistry
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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
2001
Nucleic Acids Research
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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
2011
Nucleic Acids Research
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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
2020
Nucleic Acids Research
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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
2003
Nucleic Acids Research
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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
2013
PLoS ONE
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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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