![[PukiWiki]](image/header_title.png "[PukiWiki]")
#author("2025-01-09T11:11:45+09:00","default:mbgdadm","mbgdadm") #author("2025-01-09T11:49:56+09:00","default:mbgdadm","mbgdadm") [[MBGD]] #contents //------------------- // ゲノム登録方法 //------------------- * Profile search (phenotype) [#v4b15bb9] #ref(profile_phenotype.png,left,wrap,create new genome,75%) + Click "Phenotype" tab. + Select phenotype in "List of phenotype" + The genus will be selected. + Using ">>>" you can add selected genus to the "Presence organisms" or "Abesence organisms" + Click “Analyze” to run a profile search. * Profile search (environment) [#me1d37c2] #ref(profile_env.png,left,wrap,create new genome,75%) + Click "Environment" tab. + Select phenotype in "List of environment" + The genus will be selected. + Using ">>>" you can add selected genus to the "Presence organisms" or "Abesence organisms" + Click “Analyze” to run a profile search. * Profile search (taxonomy) [#e8ea9428] #ref(profile_tax.png,left,wrap,create new genome,75%) + Click "Tax" tab. + Select phenotype in "List of taxonomy" + The genus will be selected. + Using ">>>" you can add selected genus to the "Presence organisms" or "Abesence organisms" + Click “Analyze” to run a profile search. * Profile search (MBGD ortholog cluster) [#e8ea9428] #ref(profile_clustid.png,left,wrap,create new genome,45%) + Click "MBGD ortholog cluster" tab. + Enter cluster id in MBGD ortholog cluster id. + The genus will be selected. + Using ">>>" you can add selected genus to the "Presence organisms" or "Abesence organisms" + Click “Analyze” to run a profile search. * Profile search (File) [#e8ea9428] #ref(profile_file.png,left,wrap,create new genome,45%) + Click "File" tab. + Create file according to format The file format should be comma-separated data and correspond to the following format: Column 1: Species name, genus name, taxonomy ID Column 2: Numerical value (1/0), string (A/B/O), numerical value (with freely set thresholds) Ultimately, the values will be evaluated as numbers, with 1 = presence and 0 = absence. If strings are used, conversion rules to numbers are required. Example: A/B = 1, C = 0. If thresholds are to be applied to numerical values, use the following format: # 0.5 and above to 1 # 0.2 or less to 0 # between 0.3 and 0.5 to 1 Items that belong to neither (neither presence nor absence) should be left empty. #ref(profile_file_format.png,left,wrap,create new genome,70%) + Upload your file. + Click “Analyze” to run a profile search.
