{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:24:45Z","timestamp":1761863085805},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The extension of mapped sequence tags is a common step in the analysis of single-end next-generation sequencing (NGS) data from protein localization and chromatin studies. The optimal extension can vary depending on experimental and technical conditions. Improper extension of sequence tags can obscure or mislead the interpretation of NGS results. We present an algorithm, ArchTEx (Architectural Tag Extender), which identifies the optimal extension of sequence tags based on the maximum correlation between forward and reverse tags and extracts and visualizes sites of interest using the predicted extension.<\/jats:p>\n               <jats:p>Availability and implementation: ArchTEx requires Java 1.6 or newer. Source code and the compiled program are freely available at http:\/\/sourceforge.net\/projects\/archtex\/<\/jats:p>\n               <jats:p>Contact: \u00a0mjbuck@buffalo.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts063","type":"journal-article","created":{"date-parts":[[2012,2,3]],"date-time":"2012-02-03T01:42:17Z","timestamp":1328233337000},"page":"1021-1023","source":"Crossref","is-referenced-by-count":19,"title":["ArchTEx: accurate extraction and visualization of next-generation sequence data"],"prefix":"10.1093","volume":"28","author":[{"given":"William K. M.","family":"Lai","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry, 2Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 and 3Molecular Epidemiology and Functional Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"},{"name":"1 Department of Biochemistry, 2Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 and 3Molecular Epidemiology and Functional Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"}]},{"given":"Jonathan E.","family":"Bard","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, 2Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 and 3Molecular Epidemiology and Functional Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"}]},{"given":"Michael J.","family":"Buck","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, 2Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 and 3Molecular Epidemiology and Functional Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"},{"name":"1 Department of Biochemistry, 2Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 and 3Molecular Epidemiology and Functional Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"},{"name":"1 Department of Biochemistry, 2Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 and 3Molecular Epidemiology and Functional Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,2,2]]},"reference":[{"key":"2023012512222427400_B1","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1101\/gr.115931.110","article-title":"High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans","volume":"21","author":"Ercan","year":"2011","journal-title":"Genome Res."},{"key":"2023012512222427400_B2","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/ng.530","article-title":"A map of open chromatin in human pancreatic islets","volume":"42","author":"Gaulton","year":"2010","journal-title":"Nat. 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