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FAQ

  List of FAQ:  
Global FAQ:
What is this FAQ?
In what cases will I find Metavir useful ?
Where should I start if I am completely new to Metavir ?

Technical FAQ:
What is the virome taxonomic composition tool ?
What is the phylogenetic tree generation tool ("Phylogeny") ?
How work the rarefaction curves ?
What is the virome comparison tool ?

Other questions :
Why should I register ?
How do I request a new phylogenetic marker ?

 Global FAQ: 
What is this FAQ?
The FAQ list the Frequently Asked Questions about Metavir.
In what cases will I find Metavir useful ?
The Metavir web-server helps you analyze one or several viral metagenomes (viromes).
The current state of server technology enables you to draw phylogenetic trees for the main viral families and give you tools for comparing your virome to other published datasets.
Where should I start if I am completely new to Metavir ?
To discover the range of possibilities offered by Metavir, we advise you to start with the guided tour . Furthermore, you will find dedicated help on each METAVIR page, under the help picture links help.

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 Technical FAQ: 
What is the virome taxonomic composition tool ?
The composition tool gives you a pie-chart of the taxonomic affiliations established from the virome reads. This pie-chart is produced with the GAAS tool (Angly et al., 2009) specifically developed to deal with virome sequences. More specifically, the virome is compared to a virus-only database, and the number of taxonomic affiliations is normalized by the genome length of the associated viral specie in order to compare the different number of virion-like particles initially present in the sample.
The percentage of reads used to establish the composition is indicated below the chart: be aware that in the current state of the reference viral databases, the composition may be estimated from a very low proportion of reads, and may not therefore reflect the actual composition of the global viral community in the sample.
What is the phylogenetic tree generation tool ("Phylogeny") ?
The "Phylogeny" page presents phylogenetic trees drawn from virome reads. Briefly, sequences homologous to the required marker are gathered, assembled at 98% on 35 bp, and used to generate phylogenetic trees alongside reference sequences taken from the PFAM database.
As virome reads do not cover the entire gene sequence, different phylogenetic trees are generated for each similarity zone (or cluster). Thus, a tree gallery on this page provides the 50 "best" trees generated (i.e. the 50 longest alignments). If the sampling is sufficient and the phylogentic marker is reliable, then all trees should give you the same biological information.
Phylogenetic trees can take a rather long time to generate, especially if a high number of metagenomic sequence are homologous to the marker. The procedure can take from a few hours up to a few days.
What are the rarefaction curves ?
Rarefaction curves are based on sequence clustering, where virome sequences are cross-compared to each other and two sequences are associated with the same group (or "cluster") when their similarity is equal to or higher than a chosen threshold (here 75%, 90% or 98%).
The curve itself presents the number of different clusters created (y-axis) from a given number of sequences (x-axis). When a dataset describes all the sequences present in the sample, any additional sequence will be placed in an already-existing cluster. The number of clusters will then remain steady even if the number of sequences increases, and the curve will then reach a plateau.
Rarefaction curves can only be compared for datasets with identical sequence sizes. Thus, "sampled" viromes should be used for these comparisons rather than "whole" viromes, unless you are sure that the viromes you compare present similar sequence sizes (information available on each project main page).
Rarefaction curves are usually computed in an hour for sampled viromes, and in a few hours for whole viromes, depending on the number and size of the sequences.
What is the virome comparison tool ?
The tree presented on the virome comparison page is based on tBLASTx comparison between each pair of viromes. A similarity score is computed for each comparison, and these scores are compiled into a score matrix.
This matrix is then reduced to the viromes chosen, and used to draw a tree compiling the most similar viromes.
Virome comparison should be available one day after virome upload, if the number of virome sequences is sufficient (i.e., more than 50 000).

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 Other questions: 
Why should I register ?
Registering will make it possible for you to upload your own virome, and perform all the analyses available. Furthermore, it will enable you to choose whether to kee your project "private", in which case only you can access it, or to make it "public", which means anyone can run the analyses, or download the sequences.
How do I request a new phylogenetic marker ?
If you would like to see a new phylogenetic marker added to the list, please fill out a request marker form .

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