ArticleNucleic acids research2020
TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 35 papers.
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35 citing papers in PubMed, 61 citations in OpenAlex.
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- The Psu protein of phage satellite P4 inhibits transcription termination factor ρ by forced hyper-oligomerization.Nature communications · 2025Article
- Using Phylogeny and a Conserved Genomic Neighborhood Analysis to Extract and Visualize Gene Sets Involved in Target Gene Function: The Case of [NiFe]-hydrogenase and Succinate Dehydrogenase.Microbes and environments · 2025Article
- FlhE functions as a chaperone to prevent formation of periplasmic flagella in Gram-negative bacteria.Nature communications · 2024Article
- Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria.Nature communications · 2024Article
- GenoFig: a user-friendly application for the visualization and comparison of genomic regions.Bioinformatics (Oxford, England) · 2024Article
- AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods.Briefings in bioinformatics · 2024Article
- Diverse domain architectures of CheA histidine kinase, a central component of bacterial and archaeal chemosensory systems.Microbiology spectrum · 2024Article
- Identification of nitric oxide mediated defense signaling and its microRNA mediated regulation duringPhysiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Amine-recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Sensing preferences for prokaryotic solute binding protein families.Microbial biotechnology · 2023Article
- Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor.Science advances · 2023Article
- Transmembrane Transcription Regulators Are Widespread in Bacteria and Archaea.Microbiology spectrum · 2023Article
- Five copper homeostasis gene clusters encode the Cu-efflux resistome of the highly copper-tolerantPeerJ · 2023Article
- Photoactive Yellow Protein Represents a Distinct, Evolutionarily Novel Family of PAS Domains.Journal of bacteriology · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Key steps in a computational study of protein function involve analysis of (i) relationships between homologous proteins, (ii) protein domain architecture and (iii) gene neighborhoods the corresponding proteins are encoded in. Each of these steps requires a separate computational task and sets of tools. Currently in order to relate protein features and gene neighborhoods information to phylogeny, researchers need to prepare all the necessary data and combine them by hand, which is time-consuming and error-prone. Here, we present a new platform, TREND (tree-based exploration of neighborhoods and domains), which can perform all the necessary steps in automated fashion and put the derived information into phylogenomic context, thus making evolutionary based protein function analysis more efficient. A rich set of adjustable components allows a user to run the computational steps specific to his task. TREND is freely available at http://trend.zhulinlab.org.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.