{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,20]],"date-time":"2023-02-20T06:17:30Z","timestamp":1676873850365},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences.<\/jats:p>\n               <jats:p>Availability: SCARF is freely available at http:\/\/msbarker.com\/software.htm, and is released under the open source GPLv3 license (http:\/\/www.opensource.org\/licenses\/gpl-3.0.html.<\/jats:p>\n               <jats:p>Contact: \u00a0msbarker@indiana.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp011","type":"journal-article","created":{"date-parts":[[2009,1,8]],"date-time":"2009-01-08T01:24:23Z","timestamp":1231377863000},"page":"535-536","source":"Crossref","is-referenced-by-count":11,"title":["SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses"],"prefix":"10.1093","volume":"25","author":[{"given":"Michael S.","family":"Barker","sequence":"first","affiliation":[{"name":"1 Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada and 2Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"},{"name":"1 Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada and 2Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"}]},{"given":"Katrina M.","family":"Dlugosch","sequence":"additional","affiliation":[{"name":"1 Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada and 2Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"}]},{"given":"A. Chaitanya C.","family":"Reddy","sequence":"additional","affiliation":[{"name":"1 Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada and 2Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"}]},{"given":"Sarah N.","family":"Amyotte","sequence":"additional","affiliation":[{"name":"1 Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada and 2Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"}]},{"given":"Loren H.","family":"Rieseberg","sequence":"additional","affiliation":[{"name":"1 Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada and 2Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"},{"name":"1 Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada and 2Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,1,6]]},"reference":[{"key":"2023013110114318800_B1","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1093\/molbev\/msn187","article-title":"Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years","volume":"25","author":"Barker","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"2023013110114318800_B2","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1101\/gr.1917404","article-title":"Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs","volume":"14","author":"Chevreux","year":"2004","journal-title":"Genome Res."},{"key":"2023013110114318800_B3","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in open microfabricated high density picoliter reactors","volume":"437","author":"Margulies","year":"2005","journal-title":"Nature"},{"key":"2023013110114318800_B4","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1093\/bioinformatics\/btg034","article-title":"TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets","volume":"19","author":"Pertea","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013110114318800_B5","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","article-title":"Identification of common molecular subsequences","volume":"147","author":"Smith","year":"1981","journal-title":"J. Mol. Biol."},{"key":"2023013110114318800_B6","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1089\/10665270050081478","article-title":"A greedy algorithm for aligning DNA sequences","volume":"7","author":"Zhang","year":"2000","journal-title":"J. Comput. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/535\/48984884\/bioinformatics_25_4_535.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/535\/48984884\/bioinformatics_25_4_535.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T19:50:12Z","timestamp":1675194612000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/4\/535\/251118"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,6]]},"references-count":6,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2009,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp011","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,2,15]]},"published":{"date-parts":[[2009,1,6]]}}}