Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree.
Gene duplication and loss are major driving forces in evolution. While many important genomic resources provide information on gene presence, there is a lack of tools giving equal importance to presence and absence information as well as web platforms enabling easy visual comparison of multiple domain-based protein occurrences at once. Here, we present Aquerium, a platform for visualizing genomic presence and absence of biomolecules with a focus on protein domain architectures. The web server offers advanced domain organization querying against the database of pre-computed domains for ∼26,000 organisms and it can be utilized for identification of evolutionary events, such as fusion, disassociation, duplication, and shuffling of protein domains. The tool also allows alternative inputs of custom entries or BLASTP results for visualization. Aquerium will be a useful tool for biologists who perform comparative genomic and evolutionary analyses. The web server is freely accessible at http://aquerium.utk.edu. Proteins 2016; 85:72-77. © 2016 Wiley Periodicals, Inc.
UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996.|Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996.|Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37961.
Ogun
0000-0001-9213-4070
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Adebali
UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996.|Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996.|Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37961.
Igor B
IB
Zhulin
D000818:Animals; D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D005075:Biological Evolution; D030541:Databases, Genetic; D005658:Fungi / Q000145:classification / Q000235:genetics; D017353:Gene Deletion; D020440:Gene Duplication; D016678:Genome; D023281:Genomics; D020407:Internet; D010802:Phylogeny; D000072417:Protein Domains; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D012984:Software; D013329:Structure-Activity Relationship
D011506:Proteins
domain architecture; genomic occurrence; genomic visualization; phylogenetic profile; protein; taxonomy tree