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COGNAT: a web server for comparative analysis of genomic neighborhoods

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dc.creatorKlimchuk, Olesya I.-
dc.creatorKonovalov, Kirill A.-
dc.creatorPerekhvatov, Vadim V.-
dc.creatorSkulachev, Konstantin V.-
dc.creatorDibrova, Daria V.-
dc.creatorMulkidjanian, Armen Y.-
dc.date.accessioned2018-04-30T09:17:36Z-
dc.date.available2018-04-30T09:17:36Z-
dc.date.issued2018-04-30T09:17:36Z-
dc.identifier.citationBiology Direct 12:26 (2017)-
dc.identifier.urihttps://osnadocs.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2018043016959-
dc.description.abstractBackground: 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 utili ty 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).eng
dc.relationhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700660/pdf/13062_2017_Article_196.pdf-
dc.rightsNamensnennung 4.0 International-
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/-
dc.subjectClusters of orthologous groups of proteinseng
dc.subjectOperoneng
dc.subjectPhylogenomic analysiseng
dc.subjectComparative genomicseng
dc.subjectOrthologseng
dc.subjectParalogseng
dc.subjectNADH:Quinone oxidoreductase of type 1eng
dc.subject.ddc570 - Biowissenschaften, Biologie-
dc.titleCOGNAT: a web server for comparative analysis of genomic neighborhoodsger
dc.typeEinzelbeitrag in einer wissenschaftlichen Zeitschrift [article]ger
dc.identifier.doi10.1186/s13062-017-0196-z-
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