Viral ORFeome

ViralORFeome Tutorials

Tutorials

You can find here some tutorials to use the ViralORFeome web interface.

Contents (Hide)

About the ViralORFeome user account
Searching informations in the ViralORFeome database
ViralORFeome user tools

About the ViralORFeome user account
ViralORFeome is an open public database that you can use and request without constraint.
However, you can create a personal ViralORFeome account to design your clone and/or order plasmids stored in ORFeotheque (our physical Viral ORF library).

You will have the right at any time to access, modify, rectify and delete all your personal data, provided you file by mail request with a copy of your proof of identity to .
- How can I create a ViralORFeome account?
  - To create your user account, go to the ViralORFeome home page, ViralORFeome account section, and click to the register link:
  - Complete the registry form:
  - Back to the ViralORFeome Home page, and log in with your mail and your password:
- How can I log in ViralORFeome?
  - If you have created you ViralORFeome account,in the ViralORFeome Home page,you can log in with your mail and your password:
- How can I create an ORFeotheque account?
  
  The ORFeotheque account is necessary if you intend to order ViralORFeome plasmids.
  - Log in and clik to the ORFeotheque account link in the ViralORFeome account section.
  - Complete the registry form:

Searching informations in the ViralORFeome database

Please use the ViralORFeome Menu, in front of each page to search informations in the ViralORFeome database.
- Search a Virus:
  - Click on "Viruses" tab in the ViralORFeome menu. A new page will open with several options to search a Virus:
    -by "Virus name": example Measles Virus
    -by "Taxon id": example 11234
    -by "Genus": example check deltavirus and push "Select" button
    -by "Viral ICTV": the viral ICTV for Measles Virus is Mev
    -by "Sub type": only for Influenza A virus, example H5N1.
    -by "Genbank accession number": example NC_001498
    -by "Genbank protein accession number": example NP_056918.1
    -by "Protein GI number": example 9626946
  - A help information bubble appears when you roll over image:
  - When you start to write in each Virus name, ICTV and sub type subcase, the interface will display a drop-down menu.
    Then, select the right one (virus name/ICTV/sub type).
- Search ORF cloned
  - Click on "Clones" tab in the ViralORFeome Menu. You will see this sub menu:
    
    Note that if you are connected with you ViralORFeome account, you will see a new sub menu:
    - -Search a clone: you will be redirected to a new web page, with several search criteria.
      -Retrieve all clones: you will obtain a list of all ORF cloned by I-MAP teams, ordered by viral strains.
      -Statistics: you will be redirected to a new web page, with ORF cloned statistics.
    - If you click on Search a clone you can select it:
    - -by Virus name: select a virus in the virus list, and also one or all specific products.
      -GenBank protein accession: If you know the GenBank protein accession number of a viral protein, you can type it.
      -Laboratory: search ORF cloned by laboratories that are involved in the I-MAP project.
      -ViralORFeome clone ID: it's the numeric ViralORFeome clone, specific for each ORF cloned.
      -Label: search a clone linked to its plasmid with the plasmid label.
    - If you click on Retrieve all clones, you will obtain a new page with all ORF cloned in ViralORFeome ordered by viral strains:
    - -viral strain: the viral strain that has been used for at least one cloning
      -name: the clone name (ViralICTV_ProteinNAME_#n).
      -cloneID: it's the numeric ViralORFeome clone, specific for each ORF cloned.
      -Product: the viral protein product (GenBank annotation).
      -type: cloning strategies: 0.0 for electronic, 1.0 for in pool, 2.0 for individual.
      -comments: optional comments from the I-MAP clone designer.
      -plasmids: status of the pDONR plasmid associated to this ORF clone.
    - If you click on Statistics you will obtain the ViralORFeome clone statistics.
- Search ORFeotheque plasmid
  - Click on "ORFeotheque" tab in the ViralORFeome Menu. You will see this sub menu:
    
    -If you click on Search a plasmid you can select it:
    - -by Virus name: select a virus in the virus list, and also one or all specific products (only viruses with at least one clone is shown).
      -Laboratory: search ORF cloned by laboratories that are involved in the I-MAP project.
      -Plasmid: you can select all plasmids constructed from a specific backbone (pDONR or pDEST plasmids).
      -ViralORFeome clone ID: it's the numeric ViralORFeome clone, specific for each ORF cloned.
      -Label: search the plasmid by the ORFeotheque label.
      - Example: search plasmids using HCV virus name
        
        Results page:
        
        -clone name: the clone name (ViralICTV_ProteinNAME_#n).
        -cloneID: it's the numeric ViralORFeome clone, specific for each ORF cloned.
        -product: the viral protein product (GenBank annotation).
        -plasmid name: the plasmid name.
        -selection marker: antibiotic selection marker of the plasmid.
        -type: donor or destination vector.
        -label: the plasmid ORFeotheque label
        -status: plasmid status.
        -add to cart: it depends of the plasmid status, but if it's available, you can click on the 'add to cart logo' to have it in your shopping cart.
        
        If you click to the 'plasmid name' link, a new window will open containing more informations concerning the backbone plasmid:
    -If you click on Retrieve all plasmids, you will obtain a new page with all ORFeotheque plasmids ordered by virus name:
    - If you click on the 'only available plasmids' link, you will filter the plasmid list to have only available plasmid with general or specific MTA:
      
      If you click on the 'clone name' link, you will be redirected to the clone page description:
- Search interactions
  - Tutorial in progress....

ViralORFeome user tools
- Create and design your clone
  - To create and design a specific clone, you need a ViralORFeome account. If it's the case, just log in on the ViralORFeome home page:
    
    - First we have to search the viral genome corresponding to our clone. In this tutorial it will be the Measles virus, Ichinose-B95a with the GenBank accession number NC_001498. We will use the Virus search page and search by GenBank accession number:
    
    - ViralORFeome result page:
    
    - Click on the genome image to select the protein corresponding to your ORF. A new page appears with an interactive representation of the genome:
    
    - To design the clone, click on the 'Design New Clone' button on the protein description page:
    
    - Fill required fields and generate the clone and its primers:
    - There are two methods to generate an electronic clone:
      - - the first one allows an automatic primer design according to start and end clone postions. By default, the complete ORF sequence is selected (be carefull at the GenBank annotation of polyproteins). It could also be possible to design ORF fragments (encoding functional and/or structural domains) by modifying nucleotidic start and stop positions.
      - - the second method consists of entering its own primers that were already designed. Tail (not specific sequence) corresponds to attB1.1 or attB2.1 gateway sequences for forward and reverse primers, respectively. Head (specific sequence), corresponds to 20-25 nucleotides specific to the viral ORF sequence.
    - When you click to the 'Generate' button:
      ViralORFeome will generate primers (if you have selected the method 1) or verify the inserted primers (if you inserted your primers using method 2).
    - Generate primers page:
    - -Clone: The clone name (automatically generated: ProteinNAME_ORF.#n).
      -Coordinates: BEGIN and END coordinates of the new clone.
      -Direction: Primer direction (forward or reverse).
      -Tm: the primer temperature-melting.
      -Sequence: the primer sequence .
      
      If everything is correct, click to 'Insert my clone and primers' button.
    - Insert primers and clone:
    
    Click on the clone name to be redirected to the page description of this new clone.
- Create and design variant
  - To create and design a variant, you need a ViralORFeome account. If it's the case, just log in on the ViralORFeome home page.
  - Click on 'Tools' to the ViralORFeome menu and click to Blast.
  - Paste your nucleotid sequence in FASTA, select the Nucleic viral CDS database and run the Blast:
  - In the results page, choose the most similar annotated sequence found by BLAST and click to the 'Alignment' button:
  - The alignment made by CLUSTALW highlights nucleic and proteic mutations:
  - If there is not too much mutations you can create a variant:
  - Fill required fileds and generate the variant:
  - Generate variant primers:
  - Insert the new variant:
  - and click to the variant clone name to see the page description of this new variant:
- Find my clones
  - This requires to be logged with your ViralORFeome account. The aim is to easely found your clones designed when you used the ViralORFeome interface and its tools.
  - Click on 'Clones' to the ViralORFeome menu and click to 'Find my clone'.
- Design primers using OSP
  - This tool is used to design ORF-specific Gateway® primers on sequence (typically CDS) that are pasted on the ViralORFeome page.
  - Click on 'Tools' to the ViralORFeome menu and click to 'Design primers'.
  - Paste you nucleotidic sequence and click on the 'Design primer' button.