{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:24:00Z","timestamp":1772173440772,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012732","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,2,24]],"date-time":"2025-02-24T00:00:00Z","timestamp":1740355200000}}],"reference-count":64,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2025,2,18]],"date-time":"2025-02-18T00:00:00Z","timestamp":1739836800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004871","name":"Technische Universit\u00e4t Braunschweig","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"\n Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, genotypes, or individuals. These variants can be enriched with predictions about their functional implications based on available structural annotations, i.e., gene models. Although these functional impact predictions on a per-variant basis are often accurate, some challenging cases require the simultaneous incorporation of multiple adjacent variants into this prediction process. Examples include neighboring variants which modify each other\u2019s functional impact. The Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence when predicting the effect. As a proof of concept, variants between the\n Arabidopsis thaliana<\/jats:italic>\n accessions Columbia-0 and Niederzenz-1 were annotated. NAVIP is freely available on GitHub (\n https:\/\/github.com\/bpucker\/NAVIP<\/jats:ext-link>\n ) and accessible through a web server (\n https:\/\/pbb-tools.de<\/jats:ext-link>\n ).\n <\/jats:p>","DOI":"10.1371\/journal.pcbi.1012732","type":"journal-article","created":{"date-parts":[[2025,2,18]],"date-time":"2025-02-18T13:36:36Z","timestamp":1739885796000},"page":"e1012732","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction"],"prefix":"10.1371","volume":"21","author":[{"given":"Jan-Simon","family":"Baasner","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0609-5621","authenticated-orcid":true,"given":"Andreas","family":"Rempel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dakota","family":"Howard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3321-7471","authenticated-orcid":true,"given":"Boas","family":"Pucker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,2,18]]},"reference":[{"key":"pcbi.1012732.ref001","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/j.cell.2016.05.063","article-title":"1,135 Genomes reveal the global pattern of polymorphism in arabidopsis thaliana","volume":"166","author":"C Alonso-Blanco","year":"2016","journal-title":"Cell"},{"issue":"1","key":"pcbi.1012732.ref002","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/s41467-017-00336-7","article-title":"Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement","volume":"8","author":"N Duan","year":"2017","journal-title":"Nat Commun"},{"issue":"2","key":"pcbi.1012732.ref003","doi-asserted-by":"crossref","first-page":"170068","DOI":"10.3835\/plantgenome2017.08.0068","article-title":"Resequencing of common bean identifies regions of inter\u2013gene pool introgression and provides comprehensive resources for molecular breeding","volume":"11","author":"JD Lobaton","year":"2018","journal-title":"Plant Genome"},{"issue":"1","key":"pcbi.1012732.ref004","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/s41597-021-00834-w","article-title":"Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing","volume":"8","author":"B Valliyodan","year":"2021","journal-title":"Sci Data"},{"issue":"6","key":"pcbi.1012732.ref005","doi-asserted-by":"crossref","first-page":"R61","DOI":"10.1186\/gb-2013-14-6-r61","article-title":"User guide for mapping-by-sequencing in Arabidopsis","volume":"14","author":"GV James","year":"2013","journal-title":"Genome Biol"},{"issue":"6","key":"pcbi.1012732.ref006","doi-asserted-by":"crossref","first-page":"R78","DOI":"10.1186\/gb-2014-15-6-r78","article-title":"Mapping-by-sequencing accelerates forward genetics in barley","volume":"15","author":"M Mascher","year":"2014","journal-title":"Genome Biol"},{"issue":"7","key":"pcbi.1012732.ref007","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.3390\/genes13071131","article-title":"Mapping-by-Sequencing Reveals Genomic Regions Associated with Seed Quality Parameters in Brassica napus","volume":"13","author":"HM Schilbert","year":"2022","journal-title":"Genes"},{"issue":"1","key":"pcbi.1012732.ref008","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1186\/s12864-023-09823-2","article-title":"Genomic characterization of a nematode tolerance locus in sugar beet","volume":"24","author":"K Sielemann","year":"2023","journal-title":"BMC Genomics"},{"issue":"7484","key":"pcbi.1012732.ref009","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1038\/nature12817","article-title":"The genome of the recently domesticated crop plant sugar beet (Beta vulgaris","volume":"505","author":"JC Dohm","year":"2014","journal-title":"). 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