ArticleBiology direct2017
COGNAT: a web server for comparative analysis of genomic neighborhoods.
Article in Biology direct, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families.Microbial genomics · 2024Article
- Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families.bioRxiv : the preprint server for biology · 2024Article
- Protein family neighborhood analyzer-ProFaNA.PeerJ · 2023Article
- The Phosin PptA Plays a Negative Role in the Regulation of Antibiotic Production inAntibiotics (Basel, Switzerland) · 2021Article
- COGcollator: a web server for analysis of distant relationships between homologous protein families.Biology direct · 2017Article
- Article
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Authors and funding
6 authors.
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Abstract
backgroundIn 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.
aimWe 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.
resultsHere 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.
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