{"action":"opened","issue":{"url":"https://api.github.com/repos/freezer333/biotools/issues/17","labels_url":"https://api.github.com/repos/freezer333/biotools/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/freezer333/biotools/issues/17/comments","events_url":"https://api.github.com/repos/freezer333/biotools/issues/17/events","html_url":"https://github.com/freezer333/biotools/issues/17","id":55547702,"number":17,"title":"overlapping motifs confuse results","user":{"login":"freezer333","id":5250504,"avatar_url":"https://avatars.githubusercontent.com/u/5250504?v=3","gravatar_id":"","url":"https://api.github.com/users/freezer333","html_url":"https://github.com/freezer333","followers_url":"https://api.github.com/users/freezer333/followers","following_url":"https://api.github.com/users/freezer333/following{/other_user}","gists_url":"https://api.github.com/users/freezer333/gists{/gist_id}","starred_url":"https://api.github.com/users/freezer333/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/freezer333/subscriptions","organizations_url":"https://api.github.com/users/freezer333/orgs","repos_url":"https://api.github.com/users/freezer333/repos","events_url":"https://api.github.com/users/freezer333/events{/privacy}","received_events_url":"https://api.github.com/users/freezer333/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-01-26T22:34:29Z","updated_at":"2015-01-26T22:34:29Z","closed_at":null,"body":"Aggressive overlapping can make a family of motifs span regions (for example, 3'UTR and downstream).  If downstream is not in the search, a different motif may be reported as \"best\" - if the actual best was downstream.  NM_001098169.1.1 is an example.  If downstream is not analyzed, a motif in the 3'UTR is selected (and scored).  If downstream is allowed (200nt), then the family extends into the downstream region, where a BETTER motif is found.  The family is reported as downstream, not 3'UTR.\r\n\r\nThis could be solved by assigning range by overlapped range.  In this case, the motif selected would be 3'UTR and downstream.  Its misleading though, because when downstream is not included the motif is much weaker - meaning search results for \"highly stable motifs in 3'UTR\" is misleading..\r\n\r\nTough problem..."}}