ViralORFeome FAQ

Frequently Asked Questions

This is a list of frequently asked questions. If your question is not answered on this page, feel free to contact the .

Contents (Hide)
1 About the ViralORFeome database 1.1 Short presentation 1.2 What is the architecture of the ViralORFeome system? 1.3 How frequently do you update the ViralORFeome database with new data from GenBank? 2 About the ViralORFeome interface 2.1 What are "NULL products" ? 2.2 What does "Mat_pep" means for protein name? 2.3 In a virus list, what does "segment" refer to ? 2.3 Strange characters appear in fasta file, is the file corrupted ? 2.4 About the genome browser 2.5 About tools 2.6 How can I have an access to the I-MAP interactions data ? 3 About ORFeotheque 3.1 What is ORFeotheque? 3.2 What is the price of a plasmid? 3.3 I have seen a plasmid interesting to me, how can I get it from ORFeotheque? 3.4 How can I order a plasmid in ORFeotheque? 3.5 Who can I contact ORFeotheque technical support?

Contents (Hide)

1 About the ViralORFeome database
2 About the ViralORFeome interface
3 About ORFeotheque

About the ViralORFeome database
- Short presentation:
  - The ViralORFeome database is dedicated to the establishment of a viral Open Reading Frames (ORFs) reference collection and the management of viral protein and host-cell protein interactions, identified by yeast two-hybrid screens realised by I-MAP teams (Infection-MAPping project).
- What is the architecture of the ViralORFeome system?
  - We are using the PostgreSQL DataBase Management System, release 8.2.6 to formalize and implement the ViralORFeome relational model. The server is running on a Linux operating system, the CentOS distribution.
  - Click here too see the ViralORFeome Entity Relationship Schema.
- How frequently do you update the ViralORFeome database with new data from GenBank?
  - We update every 6 months all viral sequences from GenBank. They consist of all complete genome sequences, genome segments and complete CDS of viruses which are extracted from Core Nucleotide division of GenBank.

About the ViralORFeome interface
- What are "NULL products"?
  - The viral protein product is as is it described in the GenBank entry. Thus, if the product is not specified in the GenBank entry, the ViralORfeome product is defined like "NULL products".
- What does "Mat_pep" means for protein name ?
  - The protein name is either a GenBank name (if given in the entry), or a name constructed from the CDS GenBankID. For mature peptide (produced following a co or post translational regulation, like a clivage by a protease), the name is either MatPEP_GenBankProteinID if the latter part is given, or GenBankCDSID_MatPep# otherwise.
- In a virus list, what does "segment" refer to ?
  - The segment has a one to one correspondance with each GenBank Entry. For one genome name on the virus list you can have 1 or more GenBank entry. Certain viral genomes are multi-segmented ie, the genome is composed of several sequences (for example, Influenza A Virus genome is composed of 8 cDNA segments).
- Strange characters appear in fasta file, is the file corrupted ?
  - The characters most commonly seen in sequence are A, C, G, T, and N, but there are several other valid characters that are used in clones to indicate ambiguity about the identity of certain bases in the sequence. It's not uncommon to see these "wobble" codes at polymorphic positions in DNA sequences. The following chart (IUPAC-IUB Symbols for Nucleotide Nomenclature: Cornish-Bowden (1985). Nucl. Acids Res. 13:3021-3030) lists nucleotide symbols, including those used for ambiguity:
```
 ------------------------------------------------
		Symbol    Meaning      Nucleic Acid
          		--------------------------------------
           		A            A           Adenine
           		C            C           Cytosine
           		G            G           Guanine
           		T            T           Thymine
           		U            U           Uracil
           		M          A or C
           		R          A or G        Purine
           		W          A or T
           		S          C or G
           		Y          C or T        Pyrimidine
           		K          G or T
           		V        A or C or G
           		H        A or C or T
           		D        A or G or T
           		B        C or G or T
           		X      G or A or T or C
           		N      G or A or T or C
			
```
- About the genome browser
  - We use the most popular viewer in GMOD, GBrowse: the generic genome browser (Genome Res 12: 1599-610 PubMed). The version used in the ViralORFeome database is Genome-Browser-1.68.
- Tools in ViralORFeome
  - BLAST (Basic Local Alignment Search Tool) for comparing viral CDS and protein sequences against others in public databases.
  - CLUSTALW: is a general purpose multiple sequence alignment for DNA or proteins. You can use it when you want to align your clone sequences against viral CDS sequences, and viral protein sequences.
  - Design primers using OSP: you can use it to design primer on sequence (typically CDS) that are not in the ViralORFeome database.
- How can I have an access to the I-MAP interactions data ?
  - Interaction data from I-MAP project will be progressively accessible to public. For example, all interactions identified by Y2H between hepatitis C virus proteins and human proteins can now be consulted through ViralORFeome.( "Hepatitis C virus infection network". de Chassey B et al. november 2008 Molecular Systems Biology)

About Orfeotheque

What is ORFeotheque ?
- I-MAP teams have generated a collection of viral ORFs that is cloned into pDONR and pDEST vectors (Gateway® recombination-based cloning system). Our goal is to store all of them in a dedicated repository for viral ORFeomes resource, that we called ORFeotheque. This repository is managed with the "Hospices Civils de Lyon", and is heberged in ViroBioTec.
What is the price of a plasmid?
- First ViralORFeome and ORFeotheque are for research purpose only, not for commercial use. It is a non-profit service to the scientific community.
- For academic research centers, the price for one plasmid is 95 € (charges applied when ordering plasmids are only a contribution we ask for the maintenance of the collection and the shipping of the plasmids).

I have seen a plasmid interesting to me, how can I get it from ORFeotheque?

The plasmids have different status, according to their relative importance, and collaborative state.

	Open status: this plasmid is available under a simple MTA. If it is stored, you can get it through online ordering (). If it's not yet stored, you can contact us ().
	Open status under specific agreement: this plasmid is available under a specific MTA. If you are interested to get it, you can contact us ().
	Closed status: this plasmid can not be distributed yet.

How can I order a plasmid in ORFeotheque?
- First of all, you have to create a ViralORFeome account. Then, you need to create a ORFeotheque account, which consists in giving us your shipping and billing addresses. Next, you can simply click on the 'add to cart logo' for each plasmid you are interested in. Then, click on 'checkout' logo , you will be redirected to your shopping cart. You can eventually delete any plasmid you don't want, edit your shipping/billing addresses, otherwise you can confirm your order. At last, but not least, you have to download the MTA, sign it and return it to us by mail. The order will not be processed until we receive the signed MTA.
- Plasmid ordering process:
  
  Plasmid ordering process
Who can I contact Orfeotheque technical support?
- If you have any technical question, please feel free to contact us at .