Documentation

FAQ

GreenPhylDB is:

GreenPhyl is a database for comparative genomics. This database proposes a classification of genes clustered in gene families. Our gene families give a synthetic view of various functional information (protein domain, GO, gene name, gene published) available from all its gene members. This database proposes also homologous predictions between gene family members.


GreenPhylDB is not:

GreenPhylDB is not a designed for the curation of individual sequences. Nucleic sequences are not stored in the database. The gene structure cannot be changed and therefore the quality of the sequences rely on the quality of the genome annotation provided by the genome sequencing consortia.


Frequently asked questions:

Why I could not find my gene identifier?

  • Does your gene belong to a genome available in GreenPhyl? See data sources
  • Do you use sequence identifier from genomes version presented in data sources?
  • You can use Diamond search tool to identify , using a protein or nucleic sequence, the most similar genes in the database

I am studying a gene from a species which is not present in GreenPhylDB. How can I find information for this gene?

We are doing our best to integrate as much as plant genomes as possible. However, the best way to have information additional sequences is to use Diamond search tool and select ‘dicotyledon’ or ‘monocotyledon’ depending on your gene.


Why is there no ortholog prediction for my gene.

Please check that the gene family has been analyzed. In the Gene family section, the ‘Phylogenetic analyzes’ is tagged with 'Not available' when the phylogenetic has not been performed. Please send us an email and we will do our best to analyze your gene family of interest and provide you orthologs predictions.


I could not find a gene family in GreenPhyl but this family is described in a paper that I have read. Why?

Gene family can be characterized by different names or descriptions in other databases or in the literature. That’s why we provide synonyms. You can use the search menu at the top of each page and look for a gene belonging to this family (‘Sequence id’ option) or use in this menu the ‘Annotation’ option to search genes using different keywords.

My gene falls in a cluster without name. why?

This gene family has not been annotated yet. Please do not hesitate to contact us if you have addtional information bout the cluster. You can use the link "suggest a name" locate near the gene family name


I have only a nucleic sequence. How could I find the corresponding entry in GreenPhylDB?

Use Diamond search tool with blastx option and select your species


I may have found an error or a bug. What should I do?

Please send us a detailed description of the bug. A print screen can be sometimes useful.