{"id":220,"date":"2021-12-13T15:13:58","date_gmt":"2021-12-13T15:13:58","guid":{"rendered":"https:\/\/rosslab.colostate.edu\/?page_id=220"},"modified":"2024-05-28T22:28:40","modified_gmt":"2024-05-28T22:28:40","slug":"general-description","status":"publish","type":"page","link":"https:\/\/rosslab.colostate.edu\/?page_id=220","title":{"rendered":"General Description"},"content":{"rendered":"\t\t
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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
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Prion Aggregation Prediction Algorithm (PAPA)<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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Prions are infectious proteins. PAPA is a tool our lab developed to predict prion activity from a protein’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 can be found here<\/a><\/strong>, and you can read more about PAPA here<\/a><\/strong>. A more recent version of PAPA (called mPAPA) can be found here<\/strong><\/a>, and you can read more about mPAPA here<\/strong><\/a>. 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

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Low-Complexity Domain Composition Scanner (\"LCD-Composer\")<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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Low-complexity domains “LCDs” 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 webserver can be found here<\/a><\/strong>, and you\u00a0can read more about LCD-Composer here<\/a><\/strong>\u00a0and here<\/strong><\/a>. To run large-scale analyses using LCD-Composer, you can also download our open-source scripts here<\/strong><\/a>.<\/p>

Image taken from\u00a0Cascarina\u00a0et al.<\/em> (2021)\u00a0NAR 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":"

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’s amino acid sequence. A prion […]<\/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,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"class_list":["post-220","page","type-page","status-publish","hentry","post-preview"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/rosslab.colostate.edu\/index.php?rest_route=\/wp\/v2\/pages\/220","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/rosslab.colostate.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/rosslab.colostate.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/rosslab.colostate.edu\/index.php?rest_route=\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/rosslab.colostate.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=220"}],"version-history":[{"count":7,"href":"https:\/\/rosslab.colostate.edu\/index.php?rest_route=\/wp\/v2\/pages\/220\/revisions"}],"predecessor-version":[{"id":510,"href":"https:\/\/rosslab.colostate.edu\/index.php?rest_route=\/wp\/v2\/pages\/220\/revisions\/510"}],"wp:attachment":[{"href":"https:\/\/rosslab.colostate.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=220"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}