{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T09:52:39Z","timestamp":1772963559165,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2020,6,2]],"date-time":"2020-06-02T00:00:00Z","timestamp":1591056000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["P30DK019525"],"award-info":[{"award-number":["P30DK019525"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>A number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, region-specific extraction (RSE) is characterized by the capture of long DNA fragments (15\u201320\u2009kb) by magnetic beads, after enzymatic extension of oligonucleotides hybridized to selected genomic regions. Facilitating the selection of the most appropriate capture oligos for targeting a region of interest, satisfying the properties of temperature (Tm) and entropy (\u0394G), while minimizing the formation of primer-dimers in a pooled experiment, is therefore necessary. Manual design and selection of oligos becomes very challenging, complicated by factors such as length of the target region and number of targeted regions. Here we describe, AnthOligo, a web-based application developed to optimally automate the process of generation of oligo sequences used to target and capture the continuum of large and complex genomic regions. Apart from generating oligos for RSE, this program may have wider applications in the design of customizable internal oligos to be used as baits for gene panel analysis or even probes for large-scale comparative genomic hybridization array processes. AnthOligo was tested by capturing the Major Histocompatibility Complex (MHC) of a random sample.<\/jats:p>\n                    <jats:p>The application provides users with a simple interface to upload an input file in BED format and customize parameters for each task. The task of probe design in AnthOligo commences when a user uploads an input file and concludes with the generation of a result-set containing an optimal set of region-specific oligos. AnthOligo is currently available as a public web application with URL: http:\/\/antholigo.chop.edu.<\/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\/btaa552","type":"journal-article","created":{"date-parts":[[2020,5,28]],"date-time":"2020-05-28T15:12:15Z","timestamp":1590678735000},"page":"4353-4356","source":"Crossref","is-referenced-by-count":7,"title":["AnthOligo: automating the design of oligonucleotides for capture\/enrichment technologies"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1159-8354","authenticated-orcid":false,"given":"Pushkala","family":"Jayaraman","sequence":"first","affiliation":[{"name":"Department of Pathology and Laboratory Medicine"}]},{"given":"Timothy","family":"Mosbruger","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine"}]},{"given":"Taishan","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine"}]},{"given":"Nikolaos G","family":"Tairis","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine"}]},{"given":"Chao","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Health & Informatics, The Children's Hospitals of Philadelphia , Philadelphia, PA, USA"}]},{"given":"Peter M","family":"Clark","sequence":"additional","affiliation":[{"name":"Department of Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson , Raritan, NJ, USA"}]},{"given":"Monica","family":"D\u2019Arcy","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, University of North Carolina , Chapel Hill, NC, USA"}]},{"given":"Deborah","family":"Ferriola","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine"}]},{"given":"Katarzyna","family":"Mackiewicz","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Medical University of South Carolina , Charleston, SC, USA"}]},{"given":"Xiaowu","family":"Gai","sequence":"additional","affiliation":[{"name":"Department of Pathology, Keck School of Medicine, University of Southern California , Los Angeles, CA, USA"},{"name":"Department of Pathology and Laboratory Medicine, Center for Personalized Medicine, Children\u2019s Hospital of Los Angeles , Los Angeles, CA, USA"}]},{"given":"Dimitrios","family":"Monos","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6069-804X","authenticated-orcid":false,"given":"Mahdi","family":"Sarmady","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine"},{"name":"Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,6,2]]},"reference":[{"key":"2023062312041206600_btaa552-B1","doi-asserted-by":"crossref","first-page":"E2183","DOI":"10.1073\/pnas.1714530115","article-title":"OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes","volume":"115","author":"Beliveau","year":"2018","journal-title":"Proc. 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