MyMBGD/Import_Genome_Data
[
Front page
] [
New
|
Page list
|
Search
|
Recent changes
|
Help
|
Log in
]
Start:
[[MyMBGD]]
#contents
//-------------------
// ゲノム登録方法
//-------------------
* How to add your own genome data to MBGD [#a4402bc9]
+ Click "Enter Your Data" on the MyMBGD top page.
+ Click "Create New Genome"
#ref(create_new_genome.png,left,wrap,create new genome,75%)
+ Enter the following genome information:
-- Species name: full species name (e.g. Carsonella ruddii)
-- Abbreviation Name: abbreviated species name (e.g. C. r...
-- Species code: short species code with 3-6 letters (e.g...
-- Strain: strain name to distinguish different strains.
Tip: A species code already used for an exising genome i...
-- Taxonomy ID: NCBI Taxonomy ID. To find Taxonomy ID of ...
#ref(search_taxid.gif,left,wrap,search_taxid,100%)
Now you can find the the Taxonomy ID of the strain Candid...
Taxnomy ID: 387662 ~
Press "Save", then "Ok", to save the genome record. ~
Tip: If you cannot find any appropriate taxonomy record,...
+ Next, enter the chromosome information. First, specify ...
A GenBank file containing multiple sequence entry can be ...
In the following, we choose GenBank format and press "Cre...
#ref(create_new_chromosome.png,left,wrap,create new genom...
Then, enter the chromosome information. In this case, the...
~
Check if the Status field in the "User Genome List" and t...
If your genome has multiple chromosomes, repeat this proc...
~
* Data Type: Incomplete genome + GeneTab,ProteinSeq [#ff2...
** GeneTab format [#c55b30e1]
- Header ~
-- beginning with #
-- Each line must be separated by a comma (,) or one-byte...
-- Acceptable Items(&color(red){*};required fields)
LEFT:|Header name|required fields|description|data|h
|id/locus_tag|&color(red){*};|gene ID|1_1|
|name||gene name|geneA|
|chrid/chr_acc|&color(red){*};|chromosome ID|chr1|
|from |&color(red){*};|Gene start location||
|to |&color(red){*};|Gene end location||
|dir ||Gene direction|1/-1/F/R/DIR/INV|
|type||gene type|CDS|
|descr||gene description||
- Data~
-- The data delimiter is a tab.
-- Required fields are as follows
--- id/locus_tag &color(red){*};
--- chrid &color(red){*};
--- from &color(red){*};
--- to &color(red){*};
-- If no header, the following order is used~
--- For 7 columns~
id, name, chrid, from, to, dir, desc
-- If there is a chrid, it is considered to have chromoso...
-- id must be unique
-- If only an amino acid sequence is available, specify f...
-- The id and the id of the fasta file of the gene should...
-- The chrid and the id of the fasta file of the chromoso...
End:
[[MyMBGD]]
#contents
//-------------------
// ゲノム登録方法
//-------------------
* How to add your own genome data to MBGD [#a4402bc9]
+ Click "Enter Your Data" on the MyMBGD top page.
+ Click "Create New Genome"
#ref(create_new_genome.png,left,wrap,create new genome,75%)
+ Enter the following genome information:
-- Species name: full species name (e.g. Carsonella ruddii)
-- Abbreviation Name: abbreviated species name (e.g. C. r...
-- Species code: short species code with 3-6 letters (e.g...
-- Strain: strain name to distinguish different strains.
Tip: A species code already used for an exising genome i...
-- Taxonomy ID: NCBI Taxonomy ID. To find Taxonomy ID of ...
#ref(search_taxid.gif,left,wrap,search_taxid,100%)
Now you can find the the Taxonomy ID of the strain Candid...
Taxnomy ID: 387662 ~
Press "Save", then "Ok", to save the genome record. ~
Tip: If you cannot find any appropriate taxonomy record,...
+ Next, enter the chromosome information. First, specify ...
A GenBank file containing multiple sequence entry can be ...
In the following, we choose GenBank format and press "Cre...
#ref(create_new_chromosome.png,left,wrap,create new genom...
Then, enter the chromosome information. In this case, the...
~
Check if the Status field in the "User Genome List" and t...
If your genome has multiple chromosomes, repeat this proc...
~
* Data Type: Incomplete genome + GeneTab,ProteinSeq [#ff2...
** GeneTab format [#c55b30e1]
- Header ~
-- beginning with #
-- Each line must be separated by a comma (,) or one-byte...
-- Acceptable Items(&color(red){*};required fields)
LEFT:|Header name|required fields|description|data|h
|id/locus_tag|&color(red){*};|gene ID|1_1|
|name||gene name|geneA|
|chrid/chr_acc|&color(red){*};|chromosome ID|chr1|
|from |&color(red){*};|Gene start location||
|to |&color(red){*};|Gene end location||
|dir ||Gene direction|1/-1/F/R/DIR/INV|
|type||gene type|CDS|
|descr||gene description||
- Data~
-- The data delimiter is a tab.
-- Required fields are as follows
--- id/locus_tag &color(red){*};
--- chrid &color(red){*};
--- from &color(red){*};
--- to &color(red){*};
-- If no header, the following order is used~
--- For 7 columns~
id, name, chrid, from, to, dir, desc
-- If there is a chrid, it is considered to have chromoso...
-- id must be unique
-- If only an amino acid sequence is available, specify f...
-- The id and the id of the fasta file of the gene should...
-- The chrid and the id of the fasta file of the chromoso...
Page:
![[PukiWiki]](image/header_title.png "[PukiWiki]")
