{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:28Z","timestamp":1674710428257},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: TURNIP comprises a suite of Perl scripts and modules that facilitates the resolution of microheterogeneity within hard-to-assemble repetitive DNA sequences. TURNIP was originally developed for the Saccharomyces Genome Resequencing Project (SGRP) within which the ribosomal DNA (rDNA) of 36 strains of S.cerevisiae were analysed to investigate the occurrence of potential polymorphisms. Here, \u2018partially resolved SNPs\u2019, or pSNPs, as well as indels, were found to be far more prevalent than previously suspected. More generally, the TURNIP software ascertains degrees of variation between large tandem repeats within a single locus, offering insights into mechanisms of genome stability and gene conversion in any organism for which genome sequence data are available.<\/jats:p>\n               <jats:p>Availability: The TURNIP source code, results files and online help are available at http:\/\/www.ncyc.co.uk\/software\/turnip.html .<\/jats:p>\n               <jats:p>Contact: \u00a0robert.davey@bbsrc.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq557","type":"journal-article","created":{"date-parts":[[2010,10,19]],"date-time":"2010-10-19T04:15:50Z","timestamp":1287461750000},"page":"2908-2909","source":"Crossref","is-referenced-by-count":3,"title":["TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence"],"prefix":"10.1093","volume":"26","author":[{"given":"Robert P.","family":"Davey","sequence":"first","affiliation":[{"name":"1 National Collection of Yeast Cultures, Institute of Food Research and 2Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK"},{"name":"1 National Collection of Yeast Cultures, Institute of Food Research and 2Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK"}]},{"given":"Stephen A.","family":"James","sequence":"additional","affiliation":[{"name":"1 National Collection of Yeast Cultures, Institute of Food Research and 2Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK"}]},{"given":"Jo","family":"Dicks","sequence":"additional","affiliation":[{"name":"1 National Collection of Yeast Cultures, Institute of Food Research and 2Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK"}]},{"given":"Ian N.","family":"Roberts","sequence":"additional","affiliation":[{"name":"1 National Collection of Yeast Cultures, Institute of Food Research and 2Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK"}]}],"member":"286","published-online":{"date-parts":[[2010,10,5]]},"reference":[{"key":"2023012507560580100_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped blast and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012507560580100_B2","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature07517","article-title":"Accurate whole human genome sequencing using reversible terminator chemistry","volume":"456","author":"Bentley","year":"2008","journal-title":"Nature"},{"key":"2023012507560580100_B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012507560580100_B4","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1126\/science.274.5287.546","article-title":"Life with 6000 genes","volume":"274","author":"Goffeau","year":"1996","journal-title":"Science"},{"key":"2023012507560580100_B5","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1101\/gr.084517.108","article-title":"Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing","volume":"19","author":"James","year":"2009","journal-title":"Genome Res."},{"key":"2023012507560580100_B6","doi-asserted-by":"crossref","first-page":"3821","DOI":"10.1101\/gad.12.24.3821","article-title":"Expansion and contraction of ribosomal DNA repeats in saccharomyces cerevisiae: requirement of replication fork blocking (FOB1) protein and the role of RNA polymerase I","volume":"12","author":"Kobayashi","year":"1998","journal-title":"Genes Dev."},{"key":"2023012507560580100_B7","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short DNA sequencing reads and calling variants using mapping quality scores","volume":"18","author":"Li","year":"2008","journal-title":"Genome Res."},{"key":"2023012507560580100_B8","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature07743","article-title":"Population genomics of domestic and wild yeasts","volume":"458","author":"Liti","year":"2009","journal-title":"Nature"},{"key":"2023012507560580100_B9","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1073\/pnas.76.1.410","article-title":"Yeast ribosomal DNA genes are located on chromosome-xii","volume":"76","author":"Petes","year":"1979","journal-title":"Proc. Natl Acad.Sci. USA"},{"key":"2023012507560580100_B10","doi-asserted-by":"crossref","first-page":"1599","DOI":"10.1101\/gr.403602","article-title":"The generic genome browser: a building block for a model organism system database","volume":"12","author":"Stein","year":"2002","journal-title":"Genome Res."},{"key":"2023012507560580100_B11","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/S0169-2607(01)00194-8","article-title":"TRAP: tandem repeat assembly program produces improved shotgun assemblies of repetitive sequences","volume":"70","author":"Tammi","year":"2003","journal-title":"Comput. Methods Programs Biomed."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/22\/2908\/48852368\/bioinformatics_26_22_2908.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/22\/2908\/48852368\/bioinformatics_26_22_2908.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:56:33Z","timestamp":1674633393000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/22\/2908\/228484"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10,5]]},"references-count":11,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2010,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq557","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,11,15]]},"published":{"date-parts":[[2010,10,5]]}}}