{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:22:06Z","timestamp":1773289326661,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,9]],"date-time":"2017-10-09T00:00:00Z","timestamp":1507507200000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["78081"],"award-info":[{"award-number":["78081"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Folding of eukaryotic genomes within nuclear space enables physical and functional contacts between regions that are otherwise kilobases away in sequence space. Targeted chromosome conformation capture methods (T2C, chi-C and HiCap) are capable of informing genomic contacts for a subset of regions targeted by probes. We here present HiCapTools, a software package that can design sequence capture probes for targeted chromosome capture applications and analyse sequencing output to detect proximities involving targeted fragments. Two probes are designed for each feature while avoiding repeat elements and non-unique regions. The data analysis suite processes alignment files to report genomic proximities for each feature at restriction fragment level and is isoform-aware for gene features. Statistical significance of contact frequencies is evaluated using an empirically derived background distribution. Targeted chromosome conformation capture applications are invaluable for locating target genes of disease-associated variants found by genome-wide association studies. Hence, we believe our software suite will prove to be useful for a wider user base within clinical and functional applications.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability<\/jats:title>\n                  <jats:p>https:\/\/github.com\/sahlenlab\/HiCapTools.<\/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\/btx625","type":"journal-article","created":{"date-parts":[[2017,9,29]],"date-time":"2017-09-29T19:11:01Z","timestamp":1506712261000},"page":"675-677","source":"Crossref","is-referenced-by-count":24,"title":["HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications"],"prefix":"10.1093","volume":"34","author":[{"given":"Anandashankar","family":"Anil","sequence":"first","affiliation":[{"name":"KTH \u2013 Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden"}]},{"given":"Rapolas","family":"Spalinskas","sequence":"additional","affiliation":[{"name":"KTH \u2013 Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden"}]},{"given":"\u00d6rjan","family":"\u00c5kerborg","sequence":"additional","affiliation":[{"name":"KTH \u2013 Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden"}]},{"given":"Pelin","family":"Sahl\u00e9n","sequence":"additional","affiliation":[{"name":"KTH \u2013 Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2017,10,3]]},"reference":[{"key":"2023012712333693800_btx625-B2","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1093\/bioinformatics\/btr174","article-title":"BamTools: a C\u2009++ API and toolkit for analyzing and managing BAM files","volume":"27","author":"Barnett","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012712333693800_btx625-B3","author":"Bochkanov"},{"key":"2023012712333693800_btx625-B4","doi-asserted-by":"crossref","first-page":"127.","DOI":"10.1186\/s13059-016-0992-2","article-title":"CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data","volume":"17","author":"Cairns","year":"2016","journal-title":"Genome Biol"},{"key":"2023012712333693800_btx625-B5","doi-asserted-by":"crossref","first-page":"gkw800","DOI":"10.1093\/nar\/gkw800","article-title":"Maps of context-dependent putative regulatory regions and genomic signal interactions","volume":"19","author":"Diamanti","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712333693800_btx625-B6","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2023012712333693800_btx625-B7","doi-asserted-by":"crossref","first-page":"1854","DOI":"10.1101\/gr.175034.114","article-title":"Unbiased analysis of potential targets of breast cancer susceptibility loci by capture Hi-C","volume":"24","author":"Dryden","year":"2014","journal-title":"Genome Res"},{"key":"2023012712333693800_btx625-B8","doi-asserted-by":"crossref","first-page":"734","DOI":"10.3390\/genes6030734","article-title":"Contribution of topological domains and loop formation to 3D chromatin organization","volume":"6","author":"Ea","year":"2015","journal-title":"Genes (Basel)"},{"key":"2023012712333693800_btx625-B9","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1126\/science.1105136","article-title":"The ENCODE (ENCyclopedia Of DNA Elements) Project","volume":"306","author":"ENCODE Project Consortium","year":"2004","journal-title":"Science (80-.)"},{"key":"2023012712333693800_btx625-B10","author":"Garrison","year":"2015"},{"key":"2023012712333693800_btx625-B1","first-page":"297","volume-title":"Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables","author":"Gautschi","year":"1972"},{"key":"2023012712333693800_btx625-B11","doi-asserted-by":"crossref","first-page":"6178","DOI":"10.1038\/ncomms7178","article-title":"Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci","volume":"6","author":"J\u00e4ger","year":"2015","journal-title":"Nat. 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