![[PukiWiki]](image/header_title.png "[PukiWiki]")
#author("2025-02-06T14:02:33+09:00","default:mbgdadm","mbgdadm") #author("2025-02-06T14:03:18+09:00","default:mbgdadm","mbgdadm") [[MBGD Documents]] #contents //------------------- // はじめの説明 //------------------- * Profile search [#zb0ea06f] ** Screen Explanation [#t2fc451f] #ref(Profile_top.png,left,nowrap,Profile top,50%) + Category(phenotype, environment information, taxonomy, mbgd ortholog cluster) ~ + List of items ~ + List of genus ~ The selected count is displayed ~ -- [Inversion] button: Clicking this button will invert the selection. ~ -- [Deselect] button: Clicking this button will clear the selection. ~ + Presence organism box ~ The selected count is displayed ~ + Absence organism box ~ The selected count is displayed ~ + Options ~ -- ''Max outputs:'' ~ Maximum number of results displayed ~ -- ''Tax rank for compression:'' ~ Maximum taxonomy rank for Dollo-parsimony compression of profiles. all for all rank, none for not applying the compression. ~ -- ''Similarity/dissimilarity measures:'' ~ Measures for similarity or dissimilarity of phylogenetic profiles --- Probability (one-sided): Default threshold is FDR < 0.05 ~ --- Probability (two-sided): Default threshold is FDR < 0.05 ~ --- Correlation coefficient: Default threshold is R > 0.05 ~ --- Hamming distance (normalized): Default threshold is Normalized Distance < 0.25 ~ --- Mutual information: Default threshold is MI > 0.25 ~ + [Analyze] button ~ (a) If checked, only items that are common between the added items and items already in the presence organism box will remain. ~ (b) Add the item selected in List of genus to the Presence organism box. ~ (c) Clean up the Presence organism box ~ (d) Add to the Absence organism box what is not included in the Presence organism box ~ (e) Add the item selected in List of genus to the Absence organism box. ~ (f) Clean up the Absence organism box ~ ** Search flow [#eb415739] + Select category(phenotype, environment information, taxonomy) how to refine your organism ~ #ref(Profile_pheno.png,left,nowrap,Profile top,50%) #ref(Profile_pheno.png,left,nowrap,Profile top,40%) + Selecting an item from the list will cause the corresponding genus to be selected ~ + Select genus and place it in the Presence/Absence organism box + Click [Analyze] button #ref(profile_res.png,left,nowrap,Profile top,75%) ** Category [#c06cb0b6] *** phenotype [#ha6b9bba] Select organisms using phenotype information from gold. ~ #ref(Profile_pheno.png,left,nowrap,Profile top,30%) #ref(Profile_pheno.png,left,nowrap,Profile top,40%) *** environment [#vf82b6af] Select organisms using environment information. ~ This dataset represents the "Read rate," which is calculated by aggregating the read counts of species (at the Genus rank) identified in the Meta16S analysis of SRA samples, grouped by the environmental unit (MEO) of each sample. #ref(Profile_env.png,left,nowrap,Profile env,30%) #ref(Profile_env.png,left,nowrap,Profile env,40%) *** taxonomy [#ec107c77] Select organisms using taxonomy information. #ref(Profile_tax.png,left,nowrap,Profile tax,30%) #ref(Profile_tax.png,left,nowrap,Profile tax,40%) *** MBGD ortholog cluster [#j195997b] Enter MBGD ortholog cluster id. #ref(Profile_mbgd.png,left,nowrap,Profile tax,30%) #ref(Profile_mbgd.png,left,nowrap,Profile tax,40%) *** file [#n2969caf] Please upload a file in the specified format. #ref(Profile_file.png,left,nowrap,Profile file,30%) #ref(Profile_file.png,left,nowrap,Profile file,40%) ''sample file'' ~ Comma Separated Format (genus name, value) ~ value 1= Add to presence organism box ~ value 0= Add to absence organism box ~ [[download sample.csv:https://mbgd.nibb.ac.jp/data/sample.csv]] Haloarcula,1 Halomicrobium,0 Halorhabdus,1 Halorientalis,0 Natronomonas, Haloarculaceae, Halalkalicoccus, ''file 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. ''heder format'' ~ # G = 1 (convert "G" to 1) # T = 0 (convert "T" to 0) # 0.5 and above to 1 # 0.2 or less to 0 # between 0.3 and 0.4 to 1 #ref(profile_file_format.png,left,wrap,create new genome,70%)
