{"id":46,"date":"2017-10-31T14:47:29","date_gmt":"2017-10-31T14:47:29","guid":{"rendered":"https:\/\/bussemakerlab.org\/site\/?page_id=46"},"modified":"2019-08-08T22:11:38","modified_gmt":"2019-08-08T22:11:38","slug":"software","status":"publish","type":"page","link":"https:\/\/bussemakerlab.org\/site\/software\/","title":{"rendered":"SOFTWARE"},"content":{"rendered":"<div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"background-color: rgba(255,255,255,0);background-position: center center;background-repeat: no-repeat;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-bottom: 0px;margin-top: 0px;border-width: 0px 0px 0px 0px;border-color:#eae9e9;border-style:solid;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last fusion-no-medium-visibility fusion-no-large-visibility\" style=\"margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><style type=\"text\/css\"><\/style><div class=\"fusion-title title fusion-title-1 fusion-title-center fusion-title-text fusion-title-size-one\" style=\"margin-top:0px;margin-right:0px;margin-bottom:31px;margin-left:0px;\"><div class=\"title-sep-container title-sep-container-left\"><div class=\"title-sep sep-double sep-solid\" style=\"border-color:#c4c2c2;\"><\/div><\/div><span class=\"awb-title-spacer\"><\/span><h1 class=\"title-heading-center\" style=\"margin:0;\">Software<\/h1><span class=\"awb-title-spacer\"><\/span><div class=\"title-sep-container title-sep-container-right\"><div class=\"title-sep sep-double sep-solid\" style=\"border-color:#c4c2c2;\"><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-1 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"margin-top:0px;margin-bottom:40px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;background-color:#ffffff;padding: 20px 20px 10px 20px;\"><div class=\"fusion-builder-row fusion-builder-row-inner fusion-row\"><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-0 fusion_builder_column_inner_1_4 1_4 fusion-one-fourth fusion-column-first\" style=\"width:25%;width:calc(25% - ( ( 4% ) * 0.25 ) );margin-right: 4%;margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><div class=\"imageframe-align-center\"><span class=\" fusion-imageframe imageframe-none imageframe-1 hover-type-none\"><img decoding=\"async\" width=\"320\" height=\"320\" title=\"dna-1811955_640\" src=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2019\/08\/embryos.png\" alt class=\"img-responsive wp-image-47\"\/><\/span><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-1 fusion_builder_column_inner_3_4 3_4 fusion-three-fourth fusion-column-last\" style=\"width:75%;width:calc(75% - ( ( 4% ) * 0.75 ) );margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 30px 0px 0px;\"><div class=\"fusion-text fusion-text-1\"><h2>NRLB<\/h2>\n<p>Our Java program \u201c<strong><a href=\"https:\/\/github.com\/BussemakerLab\/NRLB\" target=\"_blank\" rel=\"noopener noreferrer\">NRLB<\/a><\/strong>\u201d for constructing highly accurate feature-based biophysical protein-DNA interaction models directly from high-throughput data is available on <a href=\"https:\/\/github.com\/BussemakerLab\/NRLB\"><strong>GitHub<\/strong><\/a>. For a detailed description of the underlying method, see <a href=\"https:\/\/www.pnas.org\/content\/115\/16\/E3692\"><strong>Rastogi et al., PNAS 2018<\/strong><\/a>.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-2 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"margin-top:0px;margin-bottom:40px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;background-color:#ffffff;padding: 20px 20px 10px 20px;\"><div class=\"fusion-builder-row fusion-builder-row-inner fusion-row\"><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-2 fusion_builder_column_inner_1_4 1_4 fusion-one-fourth fusion-column-first\" style=\"width:25%;width:calc(25% - ( ( 4% ) * 0.25 ) );margin-right: 4%;margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><div class=\"imageframe-align-center\"><span class=\" fusion-imageframe imageframe-none imageframe-2 hover-type-none\"><img decoding=\"async\" width=\"320\" height=\"320\" title=\"dna-1811955_640\" src=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-1811955_640.png\" alt class=\"img-responsive wp-image-47\" srcset=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-1811955_640-200x200.png 200w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-1811955_640.png 320w\" sizes=\"(max-width: 800px) 100vw, 320px\" \/><\/span><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-3 fusion_builder_column_inner_3_4 3_4 fusion-three-fourth fusion-column-last\" style=\"width:75%;width:calc(75% - ( ( 4% ) * 0.75 ) );margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 30px 0px 0px;\"><div class=\"fusion-text fusion-text-2\"><h2>SELEX<\/h2>\n<p>Our <strong>R package \u201c<a href=\"http:\/\/bioconductor.org\/packages\/SELEX\" target=\"_blank\" rel=\"noopener noreferrer\">SELEX<\/a>\u201d<\/strong> for analyzing high-throughput protein-DNA interaction data is available on <a href=\"http:\/\/bioconductor.org\/\" target=\"_blank\" rel=\"noopener noreferrer\">Bioconductor.org<\/a>. For a detailed description of the underlying methods, see <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22153072\" target=\"_blank\" rel=\"noopener noreferrer\">Slattery et al., Cell 2011<\/a> and <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25151169\" target=\"_blank\" rel=\"noopener noreferrer\">Riley et al., 2015<\/a><\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-3 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"margin-top:0px;margin-bottom:40px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;background-color:#ffffff;padding: 20px 10px 10px 20px;\"><div class=\"fusion-builder-row fusion-builder-row-inner fusion-row\"><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-4 fusion_builder_column_inner_1_4 1_4 fusion-one-fourth fusion-column-first\" style=\"width:25%;width:calc(25% - ( ( 4% ) * 0.25 ) );margin-right: 4%;margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><div class=\"imageframe-align-center\"><span class=\" fusion-imageframe imageframe-none imageframe-3 hover-type-none\"><img decoding=\"async\" width=\"320\" height=\"320\" title=\"dna-2\" src=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-2.png\" alt class=\"img-responsive wp-image-52\" srcset=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-2-200x200.png 200w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-2.png 320w\" sizes=\"(max-width: 800px) 100vw, 320px\" \/><\/span><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-5 fusion_builder_column_inner_3_4 3_4 fusion-three-fourth fusion-column-last\" style=\"width:75%;width:calc(75% - ( ( 4% ) * 0.75 ) );margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 20px 0px 0px;\"><div class=\"fusion-text fusion-text-3\"><h2>REDUCE Suite<\/h2>\n<p>Using the latest version of our <a href=\"http:\/\/reducesuite.bussemakerlab.org\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span style=\"text-decoration: underline;\"><strong><em>REDUCE Suite<\/em><\/strong><\/span><\/a>\u00a0you can perform integrative analysis of sequence and expression data. It provides an integrated set of tools for motif discovery (\u201c<em>MatrixREDUCE<\/em>\u201d), inferring motif activities (\u201c<em>Transfactivity<\/em>\u201d), and generating sequence logos (\u201c<em>LogoGenerator<\/em>\u201d), including the \u201caffinity\/energy logos\u201d that our lab invented. The software is available by registering on our new <a href=\"http:\/\/reducesuite.bussemakerlab.org\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span style=\"text-decoration: underline;\"><strong>REDUCE Forum<\/strong><\/span><\/a>.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-4 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"margin-top:0px;margin-bottom:40px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;background-color:#ffffff;padding: 20px 20px 10px 20px;\"><div class=\"fusion-builder-row fusion-builder-row-inner fusion-row\"><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-6 fusion_builder_column_inner_1_4 1_4 fusion-one-fourth fusion-column-first\" style=\"width:25%;width:calc(25% - ( ( 4% ) * 0.25 ) );margin-right: 4%;margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><div class=\"imageframe-align-center\"><span class=\" fusion-imageframe imageframe-none imageframe-4 hover-type-none\"><img decoding=\"async\" width=\"320\" height=\"320\" title=\"dna 3\" src=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-3.jpg\" alt class=\"img-responsive wp-image-53\" srcset=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-3-200x200.jpg 200w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/10\/dna-3.jpg 320w\" sizes=\"(max-width: 800px) 100vw, 320px\" \/><\/span><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-7 fusion_builder_column_inner_3_4 3_4 fusion-three-fourth fusion-column-last\" style=\"width:75%;width:calc(75% - ( ( 4% ) * 0.75 ) );margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 30px 0px 0px;\"><div class=\"fusion-text fusion-text-4\"><h2>DSSR<\/h2>\n<p><a href=\"http:\/\/forum.x3dna.org\/rna-structures\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span style=\"text-decoration: underline;\"><strong>DSSR<\/strong><\/span><\/a>\u00a0is a new integrated software tool for dissecting the spatial structure of RNA that was developed by Xiang-Jun Lu, an Research Scientist in our lab who created the widely used <a href=\"http:\/\/x3dna.org\" target=\"_blank\" rel=\"noopener noreferrer\"><strong><em>3DNA<\/em> software<\/strong><\/a>.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"nf_dc_page":"","footnotes":""},"class_list":["post-46","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/pages\/46","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/comments?post=46"}],"version-history":[{"count":12,"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/pages\/46\/revisions"}],"predecessor-version":[{"id":230,"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/pages\/46\/revisions\/230"}],"wp:attachment":[{"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/media?parent=46"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}