{"id":162,"date":"2025-04-22T21:54:47","date_gmt":"2025-04-23T04:54:47","guid":{"rendered":"https:\/\/labs.wsu.edu\/wisecaver\/?page_id=162"},"modified":"2025-04-23T09:51:46","modified_gmt":"2025-04-23T16:51:46","slug":"tools","status":"publish","type":"page","link":"https:\/\/labs.wsu.edu\/wisecaver\/tools\/","title":{"rendered":"Tools"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Alien Index: detect HGT and contamination in genomes<\/h2>\n\n\n<div class=\"wsu-row wsu-row--sidebar-left\" >\r\n    \n<div class=\"wsu-column\"  style=\"\">\r\n\t\n<article class=\"wsu-card\">\r\n\t\t<div class=\"wsu-image-frame wsu-image--ratio-1-1\">\r\n\t\t\t\t\t<img decoding=\"async\" src=\"https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/3545\/2025\/04\/ScreenShot2018-09-13at7.54.40AM.png\"\r\n\t\t\t\tsrcset=\"https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/3545\/2025\/04\/ScreenShot2018-09-13at7.54.40AM.png 750w, https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/3545\/2025\/04\/ScreenShot2018-09-13at7.54.40AM-300x300.png 300w, https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/3545\/2025\/04\/ScreenShot2018-09-13at7.54.40AM-150x150.png 150w\"\r\n\t\t\t\tsizes=\"(max-width: 750px) 100vw, 750px\"\r\n\t\t\t\talt=\"phylogenetic tree showing horizontal gene transfer from bacteria to animals\"\r\n\t\t\t\tstyle=\"object-position: 50% 50%\"\r\n\t\t\t\/>\r\n\t\t\t<\/div>\r\n\t\t<div class=\"wsu-card__content\">\r\n\t\t\t\t\t\t\t\t\t\t\t<\/div>\r\n\t<\/article>\n<\/div>\r\n\n\n<div class=\"wsu-column\"  style=\"\">\r\n\t\n\n<p>The Alien Index (AI) is a sequence similarity based score to flag genes with significantly better hits to distantly related organisms than to closely related ones and thereby identify candidate HGT events as well as likely assembly contamination. <strong>aiViz<\/strong>, a tool for running an AI each and visualizing the results is available on our<a href=\"https:\/\/github.itap.purdue.edu\/jwisecav\/aiViz\"> GitHub<\/a>.<\/p>\n\n\n\n<p>Publications that used the Alien Index: <a href=\"https:\/\/cdn.elifesciences.org\/articles\/33034\/elife-33034-v1.pdf\">Gon\u00e7alves et al. 2018. eLife<\/a>, <a href=\"https:\/\/www.nature.com\/articles\/s41598-018-24301-6\">Zhang et al. 2018. Scientific Reports<\/a>, <a href=\"https:\/\/academic.oup.com\/mbe\/article\/33\/8\/1979\/2579218\">Wisecaver et al. 2016. MBE<\/a>, <a href=\"http:\/\/www.pnas.org\/content\/113\/15\/4116\">Alexander et al. 2016. PNAS<\/a><\/p>\n\n<\/div>\r\n\n<\/div>\n\n\n<h2 class=\"wp-block-heading\">Mutual Ranks and Modules: identify co-expressed gene sets<\/h2>\n\n\n<div class=\"wsu-row wsu-row--sidebar-left\" >\r\n    \n<div class=\"wsu-column\"  style=\"\">\r\n\t\n<article class=\"wsu-card\">\r\n\t\t<div class=\"wsu-image-frame wsu-image--ratio-1-1\">\r\n\t\t\t\t\t<img decoding=\"async\" src=\"https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/3545\/2025\/04\/ScreenShot2018-09-13at8.03.42AM.png\"\r\n\t\t\t\tsrcset=\"https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/3545\/2025\/04\/ScreenShot2018-09-13at8.03.42AM.png 750w, https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/3545\/2025\/04\/ScreenShot2018-09-13at8.03.42AM-300x300.png 300w, https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/3545\/2025\/04\/ScreenShot2018-09-13at8.03.42AM-150x150.png 150w\"\r\n\t\t\t\tsizes=\"(max-width: 750px) 100vw, 750px\"\r\n\t\t\t\talt=\"network showing cluster of coexpressed genes\"\r\n\t\t\t\tstyle=\"object-position: 50% 50%\"\r\n\t\t\t\/>\r\n\t\t\t<\/div>\r\n\t\t<div class=\"wsu-card__content\">\r\n\t\t\t\t\t\t\t\t\t\t\t<\/div>\r\n\t<\/article>\n<\/div>\r\n\n\n<div class=\"wsu-column\"  style=\"\">\r\n\t\n\n<p>Transforming Pearson\u2019s correlations into Mutual Ranks (MRs) \u2014 first described by <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19767600\">Obayashi &amp; Kinoshita<\/a> \u2014 is a good idea if you want to compare between different datasets and\/or functional categories. However, MRs range from 1 to <em>n<\/em> (where <em>n<\/em> is the number of genes in the genome), which does not translate well to network edge weights, which typically range from 1 to 0. We\u2019ve implemented exponential decay functions to transform MRs to edge weights and call co-expressed gene sets (i.e. modules) using the program <a href=\"http:\/\/www.paccanarolab.org\/cluster-one\/\">ClusterONE<\/a>. The full MR to modules workflow is available on on <a href=\"https:\/\/github.itap.purdue.edu\/jwisecav\/mr2mods\">GitHub<\/a>.<\/p>\n\n\n\n<p>Publications that used our workflow: <a href=\"https:\/\/static1.squarespace.com\/static\/59c96b9a51a584c476f1f6f1\/t\/59dc24f4a9db09b4a109ae77\/1507599609212\/Plant+Cell+2017+Wisecaver.pdf\">Wisecaver et al. 2017 Plant Cell<\/a>.<\/p>\n\n<\/div>\r\n\n<\/div>","protected":false},"excerpt":{"rendered":"<p>Alien Index: detect HGT and contamination in genomes Mutual Ranks and Modules: identify co-expressed gene sets<\/p>\n","protected":false},"author":44135,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"categories":[],"tags":[],"wsuwp_university_location":[],"wsuwp_university_org":[],"_links":{"self":[{"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/pages\/162"}],"collection":[{"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/users\/44135"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/comments?post=162"}],"version-history":[{"count":2,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/pages\/162\/revisions"}],"predecessor-version":[{"id":166,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/pages\/162\/revisions\/166"}],"wp:attachment":[{"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/media?parent=162"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/categories?post=162"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/tags?post=162"},{"taxonomy":"wsuwp_university_location","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/wsuwp_university_location?post=162"},{"taxonomy":"wsuwp_university_org","embeddable":true,"href":"https:\/\/labs.wsu.edu\/wisecaver\/wp-json\/wp\/v2\/wsuwp_university_org?post=162"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}