{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T20:20:39Z","timestamp":1783542039223,"version":"3.55.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,11,16]],"date-time":"2021-11-16T00:00:00Z","timestamp":1637020800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wellcome Trust and Cancer Research UK"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>CRISPR\/Cas9-based technology allows for the functional analysis of genetic variants at single nucleotide resolution whilst maintaining genomic context. This approach, known as saturation genome editing (SGE), a form of deep mutational scanning, systematically alters each position in a target region to explore its function. SGE experiments require the design and synthesis of oligonucleotide variant libraries which are introduced into the genome. This technology is applicable to diverse fields such as disease variant identification, drug development, structure\u2013function studies, synthetic biology, evolutionary genetics and host\u2013pathogen interactions. Here, we present the Variant Library Annotation Tool (VaLiAnT) which can be used to generate variant libraries from user-defined genomic coordinates and standard input files. The software can accommodate user-specified species, reference sequences and transcript annotations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Coordinates for a genomic range are provided by the user to retrieve a corresponding oligonucleotide reference sequence. A user-specified range within this sequence is then subject to systematic, nucleotide and\/or amino acid saturating mutator functions. VaLiAnT provides a novel way to retrieve, mutate and annotate genomic sequences for oligonucleotide library generation. Specific features for SGE library generation can be employed. In addition, VaLiAnT is configurable, allowing for cDNA and prime editing saturation library generation, with other diverse applications possible.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>VaLiAnT is a command line tool written in Python. Source code, testing data, example input and output files and executables are available (https:\/\/github.com\/cancerit\/VaLiAnT) in addition to a detailed user manual (https:\/\/github.com\/cancerit\/VaLiAnT\/wiki). VaLiAnT is licensed under AGPLv3.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab776","type":"journal-article","created":{"date-parts":[[2021,11,10]],"date-time":"2021-11-10T23:57:29Z","timestamp":1636588649000},"page":"892-899","source":"Crossref","is-referenced-by-count":9,"title":["Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments"],"prefix":"10.1093","volume":"38","author":[{"given":"Luca","family":"Barbon","sequence":"first","affiliation":[{"name":"Cancer, Ageing and Somatic Mutation Programme , Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Offord","sequence":"additional","affiliation":[{"name":"Cancer, Ageing and Somatic Mutation Programme , Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth J","family":"Radford","sequence":"additional","affiliation":[{"name":"Human Genetics Programme, Wellcome Sanger Institute, Hinxton , Cambridge CB10 1SA, UK"},{"name":"Department of Paediatrics, University of Cambridge , Cambridge CB2 0QQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam P","family":"Butler","sequence":"additional","affiliation":[{"name":"Cancer, Ageing and Somatic Mutation Programme , Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian S","family":"Gerety","sequence":"additional","affiliation":[{"name":"Human Genetics Programme, Wellcome Sanger Institute, Hinxton , Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9490-0306","authenticated-orcid":false,"given":"David J","family":"Adams","sequence":"additional","affiliation":[{"name":"Cancer, Ageing and Somatic Mutation Programme , Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong Kee","family":"Tan","sequence":"additional","affiliation":[{"name":"Human Genetics Programme, Wellcome Sanger Institute, Hinxton , Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5905-399X","authenticated-orcid":false,"given":"Andrew J","family":"Waters","sequence":"additional","affiliation":[{"name":"Cancer, Ageing and Somatic Mutation Programme , Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,16]]},"reference":[{"key":"2023020108534182200_btab776-B1","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/s41586-019-1711-4","article-title":"Search-and-replace genome editing without double-strand breaks or donor DNA","volume":"576","author":"Anzalone","year":"2019","journal-title":"Nature"},{"key":"2023020108534182200_btab776-B2","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1038\/s41551-020-00622-8","article-title":"A web tool for the design of prime-editing guide RNAs","volume":"5","author":"Chow","year":"2021","journal-title":"Nature Biomed. 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Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab776\/41904657\/btab776.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/892\/49008934\/btab776.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/892\/49008934\/btab776.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T15:14:52Z","timestamp":1675264492000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/4\/892\/6429268"}},"subtitle":[],"editor":[{"given":"Tobias","family":"Marschall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,11,16]]},"references-count":31,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2022,1,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab776","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.01.19.427318","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,2,15]]},"published":{"date-parts":[[2021,11,16]]}}}