{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T04:10:11Z","timestamp":1759205411174,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,13]],"date-time":"2020-01-13T00:00:00Z","timestamp":1578873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Cancer Center Support Grant"},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P30CA118100"],"award-info":[{"award-number":["P30CA118100"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome annotation is an important step for all in-depth bioinformatics analysis. It is imperative to augment quantity and diversity of genome-wide annotation data for the latest reference genome to promote its adoption by ongoing and future impactful studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a python toolkit AnnoGen, which at the first time, allows the annotation of three pragmatic genomic features for the GRCh38 genome in enormous base-wise quantities. The three features are chemical binding Energy, sequence information Entropy and Homology Score. The Homology Score is an exceptional feature that captures the genome-wide homology through single-base-offset tiling windows of 100 continual nucleotide bases. AnnoGen is capable of annotating the proprietary pragmatic features for variable user-interested genomic regions and optionally comparing two parallel sets of genomic regions. AnnoGen is characterized with simple utility modes and succinct HTML report of informative statistical tables and plots.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/shengqh\/annogen.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa027","type":"journal-article","created":{"date-parts":[[2020,1,9]],"date-time":"2020-01-09T04:20:05Z","timestamp":1578543605000},"page":"2899-2901","source":"Crossref","is-referenced-by-count":3,"title":["AnnoGen: annotating genome-wide pragmatic features"],"prefix":"10.1093","volume":"36","author":[{"given":"Quanhu","family":"Sheng","sequence":"first","affiliation":[{"name":"Department of Biostatistics , Vanderbilt University Medical Center, Nashville, TN 37232, USA"}]},{"given":"Hui","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine , Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, USA"}]},{"given":"Olufunmilola","family":"Oyebamiji","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine , Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, USA"}]},{"given":"Jiandong","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science , University of South Carolina, Columbia, SC 29205, USA"}]},{"given":"Danqian","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology , Western China School of Life Sciences, Northwest University, Xi'an, Shaanxi, China"}]},{"given":"Scott","family":"Ness","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine , Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, USA"}]},{"given":"Ying-Yong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology , Western China School of Life Sciences, Northwest University, Xi'an, Shaanxi, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5252-3960","authenticated-orcid":false,"given":"Yan","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine , Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,1,13]]},"reference":[{"key":"2023013111482547200_btaa027-B1","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.ymeth.2012.05.001","article-title":"Hi-C: a comprehensive technique to capture the conformation of genomes","volume":"58","author":"Belton","year":"2012","journal-title":"Methods"},{"key":"2023013111482547200_btaa027-B2","doi-asserted-by":"crossref","first-page":"e30377","DOI":"10.1371\/journal.pone.0030377","article-title":"Fast computation and applications of genome mappability","volume":"7","author":"Derrien","year":"2012","journal-title":"PLoS One"},{"key":"2023013111482547200_btaa027-B3","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.ygeno.2017.01.005","article-title":"Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis","volume":"109","author":"Guo","year":"2017","journal-title":"Genomics"},{"first-page":"639922","year":"2019","author":"Krietenstein","key":"2023013111482547200_btaa027-B4"},{"key":"2023013111482547200_btaa027-B5","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.1630","article-title":"GREAT improves functional interpretation of cis-regulatory regions","volume":"28","author":"McLean","year":"2010","journal-title":"Nat. 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