User guide

FunEVA was designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms (SNP) for large-scale genotyping studies. This tool is based on many existing tools to perform functional annotation of each variant.

FunEVA_prot module is dedicated to functional annotation and prioritization of SNVs. You can analyze :

• Variation properties
  • Amino-acid properties
  • Evolutionary analysis
  • Functional importance prediction into classes (Human only)
• Functional signatures
  • Motifs and domains
  • Regions
• Interaction, ontology and pathways
  • Structural properties
  • Protein interaction
  • Pathways
  • GO terms
• Mutations repositories links
  • OMIM
  • COSMIC
  • Ensembl Variation
  • dnSNP annotations

FunEVA requires :

• PHP5.0.0 or newer
• Apache 2.2.27 or newer
• MySQL5 or newer
• Python 2.7.3 or newer
• Perl v5.14.2 or newer

The databases installation can be done using PhpMyAdmin.
The default file upload maximal size allowed by Apache is 2Mb. Your data files sizes may be larger than this bound: ask your server administrator to increase this bound by updating the upload_max_filesize value in the php.ini configuration file of the Apache server. You can also load SQL files using Mysql in command line.

The tutorial describes detailed results, the references and publications and an example of study using FunEVA_prot module.
See tutorial.