History of MyMBGD/Import_Genome_Data (No. 4)

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MyMBGD

How to add your own genome data to MBGD†

1. Click "Enter Your Data" on the MyMBGD home page.
2. Click "Create New Genome"
3. Enter the genome information, and click "Save".
   • Species name: Carsonella ruddii
   • Abbreviation Name: C. ruddii (or just press the "Set" button)
   • Species code: u_cru
   • Strain: PV

     Tip: A species code already used for an exising genome in MBGD is not allowed. We recommend you to include digits or underscores in the species code to avoid duplicate name. To find Taxonomy ID, press the "Search the NCBI Taxonomy DB" button.

     Now you can find the the Taxonomy ID of the strain Candidatus Carsonella PV and enter it:
     Taxnomy ID: 387662
     Press "Save", then "Ok", to save the genome record.
     

     Tip: If you cannot find any appropriate taxonomy record, you can specify any taxonomy node near your organism. If you specify no taxonomy ID or a non-existing ID, your data will be treated as "Unclassified".

4. Next, enter the chromosome information. First, specify the type of your input file; for complete genome data, you can choose either a GenBank format file (GenBank) or a tab delimited gene file plus a fasta formatted protein sequence file (GeneTab+ProteinSeq). Here, we choose GenBank format and press "Create New Chromosome" button.

   You can choose from the following types.
   - GenBank
   - GeneTab + ProteinSeq

   Then, enter the information. In this case, the choromosome name is automatically assigned as "chromosome 1", but you can change it if you want. If your data is in a GenBank format file that contains all required information, then you can just enter the file name into the "Data in GenBank Format" field. Otherwise, you should see Help. After you entered information, press the "Save" button below, and press "Ok".
   
   Check if the Status field in the "User Genome List" and the "User Chromsome List" tables in the light side panel are changed from "Incomplete" to "Ok." You can also check whether the gene information in your input data is correctly read, by pressing the "View Saved Data" button. If your genome has multiple chromosomes, repeat this process until all data have been uploaded.
   
   If everything is OK, then press the "Next" button at the top right corner.
5. Click "Browse" to upload the file.

Data Type: Incomplete genome + GeneTab,ProteinSeq†

GeneTab format†

• ヘッダー条件
  
  • #で始まる
  • 項目ごとにカンマ(,)、もしくは、半角スペースで区切られていること
  • 受け入れ可能項目(*必須項目)

• データ条件
  
  • データの区切り文字はタブとする
  • 必須項目は下記
    • id/locus_id *
    • from *
    • to *
    • dir *
  • ヘッダーを付けない場合は下記の順番とする
    
    • 7カラムの場合
      id, name, from, to, dir, type, desc
    • 6カラムの場合
      id, name, from, to, dir, desc
  • chridがあればchromosome情報があるとみなす
  • idのデータは重複してはならない
  • アミノ酸配列しかない場合は、from=-1, to=-1を指定する
  • idとgeneのfastaファイルのidは対応したものを記載する
  • chridとchromosomeのfastaファイルのidは対応したものを記載する