MBGD/Profile search
[
Front page
] [
New
|
Page list
|
Search
|
Recent changes
|
Help
|
Log in
]
Start:
[[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...
+ 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...
+ 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...
+ 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...
+ 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 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...
#ref(profile_file_format.png,left,wrap,create new genome,...
+ Upload your file.
+ Click “Analyze” to run a profile search.
End:
[[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...
+ 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...
+ 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...
+ 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...
+ 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 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...
#ref(profile_file_format.png,left,wrap,create new genome,...
+ Upload your file.
+ Click “Analyze” to run a profile search.
Page:
![[PukiWiki]](image/header_title.png "[PukiWiki]")
