{"id":202,"date":"2021-12-11T20:01:43","date_gmt":"2021-12-11T20:01:43","guid":{"rendered":"https:\/\/rosslab.colostate.edu\/?page_id=202"},"modified":"2024-05-26T20:17:25","modified_gmt":"2024-05-26T20:17:25","slug":"bioinformatics-tools","status":"publish","type":"page","link":"https:\/\/rosslab.colostate.edu\/?page_id=202","title":{"rendered":"Bioinformatics Tools"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"202\" class=\"elementor elementor-202\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-70c519d elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"70c519d\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-1af9a6f\" data-id=\"1af9a6f\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-d533fd7 elementor-widget elementor-widget-heading\" data-id=\"d533fd7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Bioinformatics Tools<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-7792b77 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"7792b77\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-390f213\" data-id=\"390f213\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-f80ce4b elementor-widget elementor-widget-heading\" data-id=\"f80ce4b\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Prion Aggregation Prediction Algorithm (PAPA)<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-242dbe2 elementor-widget elementor-widget-text-editor\" data-id=\"242dbe2\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>Prions are infectious proteins. PAPA is a tool our lab developed to predict prion activity from a protein&#8217;s amino acid sequence. A prion propensity score was determined experimentally for each of the 20 canonical amino acids. These scores are then used to predict the prion propensity of a protein of interest using a sliding window and a series of averages within and across windows. In addition, known prion domains are often intrinsically disordered: therefore, PAPA preferentially scores regions that are predicted to be disordered. The original PAPA source code and webserver <strong><a href=\"https:\/\/combi.cs.colostate.edu\/supplements\/papa\/\">can be found here<\/a><\/strong>, and you <strong><a href=\"https:\/\/www.pubmed.ncbi.nlm.nih.gov\/19884345\/\">can read more about PAPA here<\/a><\/strong>. A more recent version of PAPA (called mPAPA) <strong><a href=\"https:\/\/github.com\/RossLabCSU\/mPAPA\">can be found here<\/a><\/strong>, and you <strong><a href=\"https:\/\/www.pubmed.ncbi.nlm.nih.gov\/31914925\/\">can read more about mPAPA here<\/a><\/strong>. In addition to identifying the highest-scoring window, mPAPA merges overlapping windows and can help users identify the largest domains scored as prion domains.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-9be165a\" data-id=\"9be165a\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-1092dc6 elementor-widget elementor-widget-image\" data-id=\"1092dc6\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"676\" height=\"502\" src=\"https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/PAPA-Algorithm_v2-01-1024x761.jpg\" class=\"attachment-large size-large wp-image-323\" alt=\"\" srcset=\"https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/PAPA-Algorithm_v2-01-1024x761.jpg 1024w, https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/PAPA-Algorithm_v2-01-300x223.jpg 300w, https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/PAPA-Algorithm_v2-01-768x571.jpg 768w, https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/PAPA-Algorithm_v2-01-1536x1141.jpg 1536w, https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/PAPA-Algorithm_v2-01-2048x1522.jpg 2048w, https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/PAPA-Algorithm_v2-01-676x502.jpg 676w\" sizes=\"(max-width: 676px) 100vw, 676px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-f52a8aa elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"f52a8aa\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-7c019a4\" data-id=\"7c019a4\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-c80ce28 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"c80ce28\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-e4180a6 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"e4180a6\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-a881218\" data-id=\"a881218\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-dd452d1 elementor-widget elementor-widget-image\" data-id=\"dd452d1\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img decoding=\"async\" width=\"520\" height=\"672\" src=\"https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/LCD-Composer.jpeg\" class=\"attachment-large size-large wp-image-211\" alt=\"\" srcset=\"https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/LCD-Composer.jpeg 520w, https:\/\/rosslab.colostate.edu\/wp-content\/uploads\/2021\/12\/LCD-Composer-232x300.jpeg 232w\" sizes=\"(max-width: 520px) 100vw, 520px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-e41d135\" data-id=\"e41d135\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-e77c6b5 elementor-widget elementor-widget-heading\" data-id=\"e77c6b5\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Low-Complexity Domain Composition Scanner (\"LCD-Composer\")<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d75e033 elementor-widget elementor-widget-text-editor\" data-id=\"d75e033\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>Low-complexity domains &#8220;LCDs&#8221; are regions in protein sequences that are enriched in one or a few amino acids. LCDs are involved in a variety for normal and pathological processes, including cellular stress responses, endocytosis, neurodegenerative disorders, and cancer. LCD-Composer is a tool to identify LCDs based on user-specified minimum composition criteria. LCD-Composer is extremely flexible, allowing users to specify any combination of amino acids and any minimum enrichment threshold. The LCD-Composer <strong><a href=\"https:\/\/lcd-composer.bmb.colostate.edu\/\" target=\"_blank\" rel=\"noopener\">webserver can be found here<\/a><\/strong>, and you&nbsp;<strong><a href=\"https:\/\/www.pubmed.ncbi.nlm.nih.gov\/34056598\/\">can read more about LCD-Composer here<\/a><\/strong>&nbsp;and <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36282522\/\" target=\"_blank\" rel=\"noopener\"><strong>here<\/strong><\/a>. To run large-scale analyses using LCD-Composer, you can also <a href=\"https:\/\/github.com\/RossLabCSU\/LCD-Composer\/tree\/master\/WebserverScripts\" target=\"_blank\" rel=\"noopener\"><strong>download our open-source scripts here<\/strong><\/a>.<\/p>\n<p>Image taken from&nbsp;Cascarina&nbsp;<em>et al.<\/em> (2021)&nbsp;<em>NAR Genom and Bioinform.<\/em><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Bioinformatics Tools Prion Aggregation Prediction Algorithm (PAPA) Prions are infectious proteins. PAPA is a tool our lab developed to predict prion activity from a protein&#8217;s amino acid sequence. A prion [&hellip;]<\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_monsterinsights_skip_tracking":false,"footnotes":""},"class_list":["post-202","page","type-page","status-publish","hentry","post-preview"],"aioseo_notices":[],"aioseo_head":"\n\t\t<!-- All in One SEO 5.0.0.1 - aioseo.com -->\n\t<meta name=\"description\" content=\"Bioinformatics Tools Prion Aggregation Prediction Algorithm (PAPA) Prions are infectious proteins. PAPA is a tool our lab developed to predict prion activity from a protein\u2019s amino acid sequence. A prion propensity score was determined experimentally for each of the 20 canonical amino acids. These scores are then used to predict the prion propensity of a\" \/>\n\t<meta name=\"robots\" content=\"max-image-preview:large\" \/>\n\t<link rel=\"canonical\" href=\"https:\/\/rosslab.colostate.edu\/?page_id=202\" \/>\n\t<meta name=\"generator\" content=\"All in One SEO (AIOSEO) 5.0.0.1\" \/>\n\t\t<meta property=\"og:locale\" content=\"en_US\" \/>\n\t\t<meta property=\"og:site_name\" content=\"Ross Lab -\" \/>\n\t\t<meta property=\"og:type\" content=\"article\" \/>\n\t\t<meta property=\"og:title\" content=\"Bioinformatics Tools - Ross Lab\" \/>\n\t\t<meta property=\"og:description\" content=\"Bioinformatics Tools Prion Aggregation Prediction Algorithm (PAPA) Prions are infectious proteins. PAPA is a tool our lab developed to predict prion activity from a protein\u2019s amino acid sequence. A prion propensity score was determined experimentally for each of the 20 canonical amino acids. 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