Welcome to FUNYBASE
FUNYBASE is a database dedicated to the analysis of fungal proteins extracted from complete public fungal genomes, and their classification in clusters of orthologs. The aim of the project is to build a bioinformatic resource useful to answer the following question: how many and which genes are sufficient to build robust fungal phylogenies?
For this purpose, proteins have been extracted from 31 fungal genomes and classified into families using an automated procedure (see Documentation for details). A subset of 21 genomes has subsequently been defined for which confident gene annotations were available. This dataset have been used to extract single-copy orthologous genes and to build phylogenies using both individual and concatenated alignments.
Using FUNYBASE it is possible to access to two sets of results:
- the complete protein families dataset, including orthologs and paralogs, built from the 31 fungal genomes (use the advanced search page to acces this results).
- the subset of 246 families of single-copy orthologs obtained from 21 genomes for which further phylogenic analyses have been performed. For each of these 246 families, FUNYBASE provides complete information, such as the aminoacid substitution model that best fits the data, the avaible annotation for the family, the mean percent of identity of the sequences in the family, the number of a variable sites, the aligned proteins, the corresponding phylogenetic tree and its similarity with the tree resulting from the concatenated dataset (go to othologs to view this results).
The FUNGI project is funded by
BRG (Bureau des Resources Génétiques) and started in january 2006.
Research labs associated to this project are :
Fungal genomes are issued from
NCBI,
MIPS,
JGI ,
Pasteur Institute and
INRA.
If you use
FUNYBASE please cite Aguileta et al, 2007.
