{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T12:38:30Z","timestamp":1773664710143,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The DNA in eukaryotic cells is packed into the chromatin that is composed of nucleosomes. Positioning of the nucleosome core particles on the sequence is a problem of great interest because of the role nucleosomes play in different cellular processes including gene regulation.<\/jats:p>\n               <jats:p>Using the sequence structure of 10.4 base DNA repeat presented in our previous works and nucleosome core DNA sequences database, we have derived the complete nucleosome DNA bendability matrix of Caenorhabditis elegans.<\/jats:p>\n               <jats:p>We have developed a web server named FineStr that allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them.<\/jats:p>\n               <jats:p>Availability: FineStr server is freely available for use on the web at http:\/www.cs.bgu.ac.il\/~nucleom. The site contains a help file with explanation regarding the exact usage.<\/jats:p>\n               <jats:p>Contact: \u00a0gabdank@cs.bgu.ac.il<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq030","type":"journal-article","created":{"date-parts":[[2010,1,28]],"date-time":"2010-01-28T01:13:21Z","timestamp":1264641201000},"page":"845-846","source":"Crossref","is-referenced-by-count":29,"title":["FineStr: a web server for single-base-resolution nucleosome positioning"],"prefix":"10.1093","volume":"26","author":[{"given":"Idan","family":"Gabdank","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Ben Gurion University of the Negev, Beer Sheva 84105, 2 Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel and 3 Division of Functional Genomics and Proteomics, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danny","family":"Barash","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Ben Gurion University of the Negev, Beer Sheva 84105, 2 Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel and 3 Division of Functional Genomics and Proteomics, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edward N.","family":"Trifonov","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Ben Gurion University of the Negev, Beer Sheva 84105, 2 Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel and 3 Division of Functional Genomics and Proteomics, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic"},{"name":"1 Department of Computer Science, Ben Gurion University of the Negev, Beer Sheva 84105, 2 Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel and 3 Division of Functional Genomics and Proteomics, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,1,26]]},"reference":[{"key":"2023012508011270400_B1","doi-asserted-by":"crossref","first-page":"10489","DOI":"10.1073\/pnas.90.22.10489","article-title":"Topography of the histone octamer surface - repeating structural motifs utilized in the docking of nucleosomal DNA","volume":"90","author":"Arents","year":"1993","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508011270400_B2","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/j.jmb.2006.06.051","article-title":"Nucleosome core particles containing a poly(dA\u00b7dT) sequence element exhibit a locally distorted DNA structure","volume":"361","author":"Bao","year":"2006","journal-title":"J. Mol. Biol."},{"key":"2023012508011270400_B3","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1016\/S0022-2836(02)00386-8","article-title":"Solvent mediated interactions in the structure of the nucleosome core particle at 1.9A resolution","volume":"319","author":"Davey","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2023012508011270400_B4","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1080\/07391102.2009.10507255","article-title":"Nucleosome DNA bendability matrix (C. elegans)","volume":"26","author":"Gabdank","year":"2009","journal-title":"J. Biomol. Str. 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Mol. Biol."},{"key":"2023012508011270400_B9","article-title":"Base pair stacking in nucleosome DNA and bendability sequence pattern","author":"Trifonov","year":"2009","journal-title":"J. Theor. Biol."},{"key":"2023012508011270400_B10","doi-asserted-by":"crossref","DOI":"10.1080\/073911010010524944","article-title":"Nucleosome positioning by sequence, state of the art and apparent finale","author":"Trifonov","year":"2010","journal-title":"J. Biomol. Str. 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