Annotation
From IGGP
Contents |
Instructions on how to annotate Vitis vinifera genes
Functional Annotation
Manual annotation can be done at Vitis vinifera web site at CRIBI.
A personal password is required for manual annotation, in order to keep a record of who did the modifications. All the modifications will become immediately available in the gene report and will be considered in the following queries. To obtain a personal password you should follow this link.
NB. The people participating in the annotation project, included in the list of collaborators organized by Mario Pezzotti will NOT need to fill out an MTA. Just fill out the form to obtain a password, then, instead of sending the MTA agreement, send an e-mail to Nicola Vitulo asking to activate the access. If you are not in the list of annotators, please contact Mario Pezzotti. More details on the manual annotation will be given with the password.
Access to the Vitis Vinifera web site for manual annotation
There are two main entry points: Gbrowse and Advanced query platform
The Gbrowse allows you to visualize the gene structure as well as searching for sequence similarities using Blast or Blat. The query platform allows you to fetch a gene by features or by name, using the original V1 gene names (e.g. JGVv38.222) or the new names (e.g. Vv3s0038g02440). In both cases (either Gbrowse or query), you should arrive at the “gene product report”, containing the annotation of the gene (see below). Several links allow direct connections between Gbrowse, gene report and query platform. A lot of “automatic” information is already associated to each gene.
You should focus on the “Gene prediction tracks”. The V1 prediction is divided into V1-NR (non repetitive) and V1-R (repetitive sequences). To allow a direct comparison with older data we also enclosed the V0 track. The Infernal track deals with the inference of non-coding RNAs. If you click on a gene, the physical details of the gene will be shown. Instead, if you just go over with the mouse (without clicking), then a window will pop up, allowing you to click on the annotation link (see figure on next page). The annotation link will take you to the “gene report page”, containing the automatic annotation, that we have already done. There are several categories of information (Gene ontology, Plant ontology, Sorting signals, etc.) that were inferred from similarity to known genes or patterns. There is also a “Vitis vinifera families section” where we reported similar genes found in the grape genome. This may be relevant for the analysis of gene families. In the “New generation sequencing” tracks you can select the SOLiD RNA-Seq analysis (strand specific) of leaf and root.
This interface allows you to do complex queries. You can select any combination of metabolic pathways, protein domains, ontologies, and more. After the selection of any number of features, the program will return a ranked list of hits, showing how many features and which satisfy your request. For instance, if three features were selected the program will tell you how many genes scored 3, 2 and 1, according to the number of satisfied features; then you can select which classes of score you want to see (for instance you could select score 3 and 2) and submit the request to obtain the list of genes. For each gene you will see which feature were satisfied. Click over the link to get the gene report page. Features set as “mandatory” must be present. To search by gene name select the “General” tab.
Click [here] to see gene annotation workflow
The tutorial for the gene annotation can be found [here].
Structural Annotation
URGI (Unité de Recherche Génomique Info) is a research unit in genomics and bioinformatics at Institut National de la Recherche Agronomique ( INRA ), dedicated to plant and crop parasites. The URGI research activity covers genome structure and dynamics. URGI hosts a bioinformatics platform , which belongs to the French national network of bioinformatics platforms ( ReNaBi ).
URGI has developed a system for manual curation of the gene model structure obtained from the automatic annotation (Apollo editing tool linked to a chado database). The access to Apollo is restricted to the grapevine annotators community upon request on our website for a login and password.In this system, the V1 annotation from Giorgio Valle was added.
[(http://urgi.versailles.inra.fr/index.php/urgi/Tools/Apollo)] to access the URGI manual curation.
Mario Pezzotti is monitoring this page.
