Tutorials |
| You can find here some tutorials to use the ViralORFeome web interface. |
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Contents (Hide) |
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-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
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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).



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.
-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.


-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.


-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 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:










-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.



















