COGNAT: a web server for comparative analysis of genomic neighborhoods
Abstract Background In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gen...
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doaj-2572dc15872a4fc1883e8320e4992e602020-11-24T21:12:48ZengBMCBiology Direct1745-61502017-11-011211710.1186/s13062-017-0196-zCOGNAT: a web server for comparative analysis of genomic neighborhoodsOlesya I. Klimchuk0Kirill A. Konovalov1Vadim V. Perekhvatov2Konstantin V. Skulachev3Daria V. Dibrova4Armen Y. Mulkidjanian5School of Bioengineering and Bioinformatics, Lomonosov Moscow State UniversitySchool of Chemistry, Lomonosov Moscow State UniversityBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversitySchool of Bioengineering and Bioinformatics, Lomonosov Moscow State UniversityAbstract Background In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. Aim We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Results Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). Reviewers This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.http://link.springer.com/article/10.1186/s13062-017-0196-zClusters of orthologous groups of proteinsOperonPhylogenomic analysisComparative genomicsOrthologsParalogs |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Olesya I. Klimchuk Kirill A. Konovalov Vadim V. Perekhvatov Konstantin V. Skulachev Daria V. Dibrova Armen Y. Mulkidjanian |
spellingShingle |
Olesya I. Klimchuk Kirill A. Konovalov Vadim V. Perekhvatov Konstantin V. Skulachev Daria V. Dibrova Armen Y. Mulkidjanian COGNAT: a web server for comparative analysis of genomic neighborhoods Biology Direct Clusters of orthologous groups of proteins Operon Phylogenomic analysis Comparative genomics Orthologs Paralogs |
author_facet |
Olesya I. Klimchuk Kirill A. Konovalov Vadim V. Perekhvatov Konstantin V. Skulachev Daria V. Dibrova Armen Y. Mulkidjanian |
author_sort |
Olesya I. Klimchuk |
title |
COGNAT: a web server for comparative analysis of genomic neighborhoods |
title_short |
COGNAT: a web server for comparative analysis of genomic neighborhoods |
title_full |
COGNAT: a web server for comparative analysis of genomic neighborhoods |
title_fullStr |
COGNAT: a web server for comparative analysis of genomic neighborhoods |
title_full_unstemmed |
COGNAT: a web server for comparative analysis of genomic neighborhoods |
title_sort |
cognat: a web server for comparative analysis of genomic neighborhoods |
publisher |
BMC |
series |
Biology Direct |
issn |
1745-6150 |
publishDate |
2017-11-01 |
description |
Abstract Background In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. Aim We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Results Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). Reviewers This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin. |
topic |
Clusters of orthologous groups of proteins Operon Phylogenomic analysis Comparative genomics Orthologs Paralogs |
url |
http://link.springer.com/article/10.1186/s13062-017-0196-z |
work_keys_str_mv |
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