MBGD/Introduction/Profile_search
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Start:
[[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, ...
+ List of items ~
+ List of genus ~
The selected count is displayed ~
-- [Inversion] button: Clicking this button will invert t...
-- [Deselect] button: Clicking this button will clear the...
+ 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 ...
-- ''Similarity/dissimilarity measures:'' ~
Measures for similarity or dissimilarity of phylogenetic ...
--- Probability (one-sided): Default threshold is FDR < 0...
--- Probability (two-sided): Default threshold is FDR < 0...
--- Correlation coefficient: Default threshold is R > 0.0...
--- Hamming distance (normalized): Default threshold is N...
--- Mutual information: Default threshold is MI > 0.25 ~
+ [Analyze] button ~
(a) If checked, only items that are common between the ad...
(b) Add the item selected in List of genus to the Presenc...
(c) Clean up the Presence organism box ~
(d) Add to the Absence organism box what is not included ...
(e) Add the item selected in List of genus to the Absence...
(f) Clean up the Absence organism box ~
** Search flow [#eb415739]
+ Select category(phenotype, environment information, tax...
#ref(Profile_pheno.png,left,nowrap,Profile top,40%)
+ Selecting an item from the list will cause the correspo...
+ Select genus and place it in the Presence/Absence organ...
+ 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,40%)
*** environment [#vf82b6af]
Select organisms using environment information. ~
This dataset represents the "Read rate," which is calcula...
aggregating the read counts of species (at the Genus rank...
in the Meta16S analysis of SRA samples, grouped by
the environmental unit (MEO) of each sample.
#ref(Profile_env.png,left,nowrap,Profile env,40%)
*** taxonomy [#ec107c77]
Select organisms using taxonomy information.
#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,40%)
*** file [#n2969caf]
Please upload a file in the specified format.
#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...
Haloarcula,1
Halomicrobium,0
Halorhabdus,1
Halorientalis,0
Natronomonas,
Haloarculaceae,
Halalkalicoccus,
''file format'' ~
The file format should be comma-separated data and corr...
Column 1: Species name, genus name, taxonomy ID
Column 2: Numerical value (1/0), string (A/B/O), nume...
Ultimately, the values will be evaluated as numbe...
If strings are used, conversion rules to numbers ...
If thresholds are to be applied to numerical valu...
# 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 abse...
''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,...
End:
[[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, ...
+ List of items ~
+ List of genus ~
The selected count is displayed ~
-- [Inversion] button: Clicking this button will invert t...
-- [Deselect] button: Clicking this button will clear the...
+ 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 ...
-- ''Similarity/dissimilarity measures:'' ~
Measures for similarity or dissimilarity of phylogenetic ...
--- Probability (one-sided): Default threshold is FDR < 0...
--- Probability (two-sided): Default threshold is FDR < 0...
--- Correlation coefficient: Default threshold is R > 0.0...
--- Hamming distance (normalized): Default threshold is N...
--- Mutual information: Default threshold is MI > 0.25 ~
+ [Analyze] button ~
(a) If checked, only items that are common between the ad...
(b) Add the item selected in List of genus to the Presenc...
(c) Clean up the Presence organism box ~
(d) Add to the Absence organism box what is not included ...
(e) Add the item selected in List of genus to the Absence...
(f) Clean up the Absence organism box ~
** Search flow [#eb415739]
+ Select category(phenotype, environment information, tax...
#ref(Profile_pheno.png,left,nowrap,Profile top,40%)
+ Selecting an item from the list will cause the correspo...
+ Select genus and place it in the Presence/Absence organ...
+ 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,40%)
*** environment [#vf82b6af]
Select organisms using environment information. ~
This dataset represents the "Read rate," which is calcula...
aggregating the read counts of species (at the Genus rank...
in the Meta16S analysis of SRA samples, grouped by
the environmental unit (MEO) of each sample.
#ref(Profile_env.png,left,nowrap,Profile env,40%)
*** taxonomy [#ec107c77]
Select organisms using taxonomy information.
#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,40%)
*** file [#n2969caf]
Please upload a file in the specified format.
#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...
Haloarcula,1
Halomicrobium,0
Halorhabdus,1
Halorientalis,0
Natronomonas,
Haloarculaceae,
Halalkalicoccus,
''file format'' ~
The file format should be comma-separated data and corr...
Column 1: Species name, genus name, taxonomy ID
Column 2: Numerical value (1/0), string (A/B/O), nume...
Ultimately, the values will be evaluated as numbe...
If strings are used, conversion rules to numbers ...
If thresholds are to be applied to numerical valu...
# 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 abse...
''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,...
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