{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T20:43:17Z","timestamp":1777581797113,"version":"3.51.4"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,12,28]],"date-time":"2016-12-28T00:00:00Z","timestamp":1482883200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"European Commission project EuroSyStem","award":["200270"],"award-info":[{"award-number":["200270"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>DNA barcodes are commonly used for counting and discriminating purposes in molecular and cell biology. Not every set of DNA sequences is equally suitable for this goal. There is a growing demand for more sophisticated barcode designs, with only few tools available. We prepared an R package that combines known algorithms and innovative methods for the efficient, flexible and near-optimal generation of robust barcode sets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our R-software package \u2018DNABarcodes\u2019 generates sets of DNA barcodes from a few basic input parameters (e.g. length, distance metric, minimum distance, chemical properties). It satisfies the specifics of most particular experimental demands in de novo design of barcodes. Additionally, the package allows analysing existing sets of DNA barcodes as well as the generation of subsets of those existing sets to improve their error correction and detection properties. \u2018DNABarcodes\u2019 was designed for speed, versatility, provable correctness and large set sizes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The DNABarcodes R package is available from Bioconductor at http:\/\/bioconductor.org\/packages\/DNABarcodes under the GPL-2 license.<\/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\/btw759","type":"journal-article","created":{"date-parts":[[2016,11,25]],"date-time":"2016-11-25T12:05:45Z","timestamp":1480075545000},"page":"920-922","source":"Crossref","is-referenced-by-count":46,"title":["DNABarcodes: an R package for the systematic construction of DNA sample tags"],"prefix":"10.1093","volume":"33","author":[{"given":"Tilo","family":"Buschmann","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,12,28]]},"reference":[{"key":"2023020204512740800_btw759-B1","author":"Ashlock","year":"2002"},{"key":"2023020204512740800_btw759-B2","volume-title":"The Systematic Design and Application of Robust DNA Barcodes","author":"Buschmann","year":"2016"},{"key":"2023020204512740800_btw759-B3","doi-asserted-by":"crossref","first-page":"272.","DOI":"10.1186\/1471-2105-14-272","article-title":"Levenshtein error-correcting barcodes for multiplexed DNA sequencing","volume":"14","author":"Buschmann","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023020204512740800_btw759-B4","doi-asserted-by":"crossref","first-page":"e36852.","DOI":"10.1371\/journal.pone.0036852","article-title":"Generalized DNA barcode design based on hamming codes","volume":"7","author":"Bystrykh","year":"2012","journal-title":"PloS One"},{"key":"2023020204512740800_btw759-B5","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1109\/TIT.1986.1057187","article-title":"Lexicographic codes: error-correcting codes from game theory","volume":"32","author":"Conway","year":"1986","journal-title":"IEEE Trans. Inf. Theor"},{"key":"2023020204512740800_btw759-B6","doi-asserted-by":"crossref","first-page":"e42543.","DOI":"10.1371\/journal.pone.0042543","article-title":"Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels","volume":"7","author":"Faircloth","year":"2012","journal-title":"PLoS ONE"},{"key":"2023020204512740800_btw759-B7","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-10-362","article-title":"Barcrawl and bartab: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing","volume":"10","author":"Frank","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023020204512740800_btw759-B8","doi-asserted-by":"crossref","first-page":"pdb.prot5448.","DOI":"10.1101\/pdb.prot5448","article-title":"Illumina sequencing library preparation for highly multiplexed target capture and sequencing","volume":"2010","author":"Meyer","year":"2010","journal-title":"Cold Spring Harbor Protoc"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/6\/920\/49038230\/bioinformatics_33_6_920.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/6\/920\/49038230\/bioinformatics_33_6_920.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:54:25Z","timestamp":1675313665000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/6\/920\/2804018"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,12,28]]},"references-count":8,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2017,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw759","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,3,15]]},"published":{"date-parts":[[2016,12,28]]}}}