{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T02:04:19Z","timestamp":1791425059586,"version":"4.3.3"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T00:00:00Z","timestamp":1715731200000},"content-version":"vor","delay-in-days":49,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2019-04266"],"award-info":[{"award-number":["RGPIN-2019-04266"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The analysis and comparison of gene neighborhoods is a powerful approach for exploring microbial genome structure, function, and evolution. Although numerous tools exist for genome visualization and comparison, genome exploration across large genomic databases or user-generated datasets remains a challenge. Here, we introduce AnnoView, a web server designed for interactive exploration of gene neighborhoods across the bacterial and archaeal tree of life. Our server offers users the ability to identify, compare, and visualize gene neighborhoods of interest from 30 238 bacterial genomes and 1672 archaeal genomes, through integration with the comprehensive Genome Taxonomy Database and AnnoTree databases. Identified gene neighborhoods can be visualized using pre-computed functional annotations from different sources such as KEGG, Pfam and TIGRFAM, or clustered based on similarity. Alternatively, users can upload and explore their own custom genomic datasets in GBK, GFF or CSV format, or use AnnoView as a genome browser for relatively small genomes (e.g. viruses and plasmids). Ultimately, we anticipate that AnnoView will catalyze biological discovery by enabling user-friendly search, comparison, and visualization of genomic data. AnnoView is available at http:\/\/annoview.uwaterloo.ca<\/jats:p>","DOI":"10.1093\/bib\/bbae229","type":"journal-article","created":{"date-parts":[[2024,4,26]],"date-time":"2024-04-26T15:37:22Z","timestamp":1714145842000},"source":"Crossref","is-referenced-by-count":22,"title":["AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods"],"prefix":"10.1093","volume":"25","author":[{"given":"Xin","family":"Wei","sequence":"first","affiliation":[{"name":"Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo , 200 University Avenue West, Waterloo, ON N2L 3G1 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huagang","family":"Tan","sequence":"additional","affiliation":[{"name":"Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo , 200 University Avenue West, Waterloo, ON N2L 3G1 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Briallen","family":"Lobb","sequence":"additional","affiliation":[{"name":"Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo , 200 University Avenue West, Waterloo, ON N2L 3G1 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Zhen","sequence":"additional","affiliation":[{"name":"Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo , 200 University Avenue West, Waterloo, ON N2L 3G1 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zijing","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo , 200 University Avenue West, Waterloo, ON N2L 3G1 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donovan H","family":"Parks","sequence":"additional","affiliation":[{"name":"Australian Centre for Ecogenomics , School of Chemistry and Molecular Biosciences, , St Lucia, QLD 4072, Brisbane , Australia"},{"name":"University of Queensland , School of Chemistry and Molecular Biosciences, , St Lucia, QLD 4072, Brisbane , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josh D","family":"Neufeld","sequence":"additional","affiliation":[{"name":"Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo , 200 University Avenue West, Waterloo, ON N2L 3G1 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"Moreno-Hagelsieb","sequence":"additional","affiliation":[{"name":"Department of Biology, Wilfrid Laurier University , 75 University Avenue West, Waterloo, ON , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew C","family":"Doxey","sequence":"additional","affiliation":[{"name":"Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo , 200 University Avenue West, Waterloo, ON N2L 3G1 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,5,14]]},"reference":[{"key":"2024051508254084900_ref1","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1101\/gr.10.8.1204","article-title":"Predicting protein function by genomic context: quantitative evaluation and qualitative inferences","volume":"10","author":"Huynen","year":"2000","journal-title":"Genome Res"},{"key":"2024051508254084900_ref2","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1038\/nbt988","article-title":"Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs","volume":"22","author":"Korbel","year":"2004","journal-title":"Nat Biotechnol"},{"key":"2024051508254084900_ref3","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1038\/76443","article-title":"Who\u2019s your neighbor? 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