{"id":2,"date":"2017-04-24T04:39:23","date_gmt":"2017-04-24T04:39:23","guid":{"rendered":"http:\/\/p512.usc.edu\/request\/?page_id=2"},"modified":"2023-04-12T13:40:46","modified_gmt":"2023-04-12T20:40:46","slug":"submit-a-new-request","status":"publish","type":"page","link":"https:\/\/p512.usc.edu\/request\/","title":{"rendered":"HIITE"},"content":{"rendered":"<p><script src=\"https:\/\/ajax.googleapis.com\/ajax\/libs\/jquery\/1.8.2\/jquery.min.js\"><\/script><\/p>\n<p><script src=\"\/hiite\/compact.js\"><\/script><\/p>\n<div>\nHIITE designates the infection stage as either being chronic or incident, and approximates the infection time of those incident subjects. Users can directly upload a single fasta file (number of sequences > 4) onto HITTE for instantaneous processing and output execution. HIITE takes two types of input: i) full envelope gene sequences and ii) envelope gene segment of HXB2 7134-7499 (check \u201cHXB2 7134-7499\u201d option). Check the \u201cAlign\u201d command if input sequences need to be aligned [<a href=\"https:\/\/link.springer.com\/chapter\/10.1007\/3-540-58094-8_5\">link<\/a>]. HIITE\u2019s output includes the stage of infection (chronic or incident) along with the Hamming distance distribution plot, diversity, genome similarity index (<a href=\"\/request\/GSI\">GSI<\/a>), and variance. For incident infection cases, estimated days post infection with 95% prediction intervals are provided. <\/p>\n<div class=\"form\">\n<form id=\"ss-single-input-form\" name=\"ss-single-input-form\">\n                <br \/>\n                Upload a Fasta File: <input type='file' id='fastafile' name=\"fastafile\" ><\/p>\n<div>\n                    Align: <input type='checkbox' id='align' name=\"align\" value=\"True\">\n                <\/div>\n<div>\n                    HXB2 7134-7499: <input type='checkbox' id='hxb2' name=\"hxb2\" value=\"True\">\n                <\/div>\n<div>\n                    <br \/>\n                    <input type='submit' value='submit' onclick=\"return upload(this.parentNode.parentNode)\">\n                <\/div>\n<\/form>\n<\/div>\n<div class=\"progress\">\n<div class=\"percent\"><\/div >\n<div class=\"bar\"><\/div >\n<\/div>\n<p><script>\nvar browser=get_browser();\nif(browser.name=='IE'){\nif(browser.version<10){\n      $('.form').html('<b>Error:<\/b> Your current browser (IE9 or older) is not supported. Please use a newer version. Also you may use another browser such as Firefox or Chrome.');\n}\n}\n<\/script><\/p>\n<p><b>Reference: <\/b> S. Y. Park, T. M. T. Love, S. Kapoor, and H. Y. Lee, HIITE: HIV-1 Incidence and Infection Time Estimator.<i>Bioinformatics.<\/i> 2018 Jun 15;34(12):2046-2052. doi: <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/bty073\">10.1093\/bioinformatics\/bty073<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>HIITE designates the infection stage as either being chronic or incident, and approximates the infection time of those incident subjects. Users can directly upload a single fasta file (number of sequences > 4) onto HITTE for instantaneous processing and output [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/page_fullwidth.php","meta":{"footnotes":""},"class_list":["post-2","page","type-page","status-publish","hentry","clearfix"],"_links":{"self":[{"href":"https:\/\/p512.usc.edu\/request\/wp-json\/wp\/v2\/pages\/2","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/p512.usc.edu\/request\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/p512.usc.edu\/request\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/p512.usc.edu\/request\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/p512.usc.edu\/request\/wp-json\/wp\/v2\/comments?post=2"}],"version-history":[{"count":31,"href":"https:\/\/p512.usc.edu\/request\/wp-json\/wp\/v2\/pages\/2\/revisions"}],"predecessor-version":[{"id":164,"href":"https:\/\/p512.usc.edu\/request\/wp-json\/wp\/v2\/pages\/2\/revisions\/164"}],"wp:attachment":[{"href":"https:\/\/p512.usc.edu\/request\/wp-json\/wp\/v2\/media?parent=2"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}