How to upload/import data in plasmid module? - LabCollector

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How to upload/import data in plasmid module?

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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 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 below steps:-

1. GeneBank data search 

  • 1a. Search GenBank Data and import the file 
  • 1b. Create plasmid with imported data

2. Uploading GenBank File

  • 1a. Upload sequences
  • 1b. Upload Plasmids

1. GeneBank data search

Go to PLASMIDS 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 Ti Plasmid from Agrobacterium Tumefaciens.
    2. You will find several results related to the search of the respective plasmid. 
    You can choose the plasmid of your choice OR you can select all the plasmids in the list and click on ‘Add to LabCollector DB”.
    The plasmid will be seen in the records of the sequence module as it is a Fasta file containing sequence information.
    3. Once you find the plasmid 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.

  • 1b. Create plasmid with imported data

  • 1. As the data is imported in the ‘Sequence module’ you can go to this module and check the file that is been imported.
    2. Click on the “Display sequence and Bioinformatic tools” option.
    3. Select the complete sequence in the box and “Copy” it.

    4. Go to the “Plasmid module” and click on
    Enter all the details for the plasmid you want to create, for example, Ti Plasmid-H. sapiens.
    5. Then go to the “Sequence and map” option.
    6.Paste” the copied sequence from the sequence module.

 

  • When you go back to the plasmid module you will see the new record with a plasmid map automatically created with copy-pasted GenBank data.

2. Uploading GenBank File

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

  • 1a. 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.

 

  • The Upload sequence is connected to the “Sequence module”, where you can upload the sequences for the plasmid that you want.
  • *The below is just an example using the Addgene website. You can use any other website or file that you want.
    Select the plasmid of your choice, such as “Ecoli RaPID plasmid”.
    On the Addgene website when you click on the plasmid name you will see the link to the SEQUENCE INFORMATION.

  • When you click on it you can perform 2 functions to import the sequence data.

    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.

  • To create a plasmid map from this sequence information you can follow the same steps as in section “1b. Create plasmid with imported data”
TIPS
– You can upload the .gb, .gbk, .ape, .txt file from the 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.

 

  • 1b. 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 “1a. 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 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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