How to upload/import data in plasmid & sequence modules? – LabCollector

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How to upload/import data in plasmid & sequence modules?

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SUMMARY:

The plasmid module offers you to add plasmid data (sequence) in the module. This saves you the hassle of creating a plasmid map from the start. 
Moreover, if you are adding a plasmid with a similar structure to a commonly known plasmid, you can add the sequence information from GenBank and then edit it in the ‘Plasmid Map Editor’.

You can easily import plasmids by following the steps below:

1. GeneBank data search for sequence ONLY

  • 1a. Search GenBank Data and import the file 

2. Uploading GenBank File

  • 2a. Upload sequences
  • 2b. Upload Plasmids

1. GeneBank data search

Go to SEQUENCES MODULE ->

  • 1a. Search GenBank Data and import the file 

  • 1. Here you will see a tab for GeneBank search. You can directly add a keyword and search for data.
    For example, if you want to search for sequence for Agrobacterium tumefaciens.
    2.You will find several results related to the search of the respective sequence. 
    You can choose the sequence of your choice OR you can select all the sequence in the list and click on ‘Add to LabCollector DB”.
    The sequence will be seen in the records of the sequence module as it is a Fasta file containing sequence information.
    3. Once you find the sequence you are looking for, you can click on ‘Add to LabCollector DataBase (DB)”.
    NOTE:  If you click on then all the search results will get selected.

    2. Uploading GenBank File

    When you go to PLASMIDS OR SEQUENCES MODULES ->, you will see two options: Upload “sequences” and “Plasmids”.

    • 2a. Upload sequences

    NOTE: This option is connected to the “Sequence module” and not the plasmid module. So anything uploaded here will be uploaded in the sequence module.

    1. You can either download the GenBank file (.gbk or .gb) and upload this file in the upload sequence option.
    2. You can copy the entire sequence and paste in, for example, notepad application and save as a .txt file. This .txt file can then be uploaded in the upload sequence option.

    TIPS
    – You can upload the .gb, .gbk, .ape, .txt file from the website of your choice.
    – You can also save the file in txt format by renaming the file and replacing the .gb /.gbk extension by .txt.

     

    • 2b. Upload Plasmids

    NOTE: This option is connected to the “Plasmids module“. So anything uploaded here will be uploaded in the plasmid module.

     

    • The Upload Plasmids option is connected to the “plasmid module”, where you can upload the sequences for the plasmid that you want.
    • You can follow the same steps as in section “2a. Upload sequences“.
    • When you upload the file the plasmid map will automatically be created from the imported file.
    TIPS
    – You can upload the .gb, .gbk, .ape, .txt file from the plasmid website of your choice.
    – You can also save the file in txt format by renaming the file and replacing the .gb /.gbk extension by .txt.

     

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