Last automatic sequence update: 1st june 2014Last manual curation: 10th dec 201313891 sequences in the database
PHYMYCO-DB is a database designed to help the mycologist community to access to fungal DNA markers data for phylogenetic analyses. Quality checked nucleotide sequences as well as manually cross-checked alignments, are available for each fungal phylum.
All candidate SSU rRNA and EF-1-α gene sequences from all fungal phyla are extracted from GenBank (NCBI). Gene sequences are filtered depending on different constraints (length, number of undetermined nucleotides, presence of long gap in the alignments...) and are locally stored in a relational database system. Sequences are regularly cross-checked by experts curators and poor quality sequences are removed from the dataset.
The content of the database is automatically updated 4 times per year.
This tool has been developed by the GenOuest platform in collaboration with the UMR 6553 Ecobio of the University of Rennes 1.
From our website, users can :
- Download fungal sequences using our taxonomic browser. - Execute an alignment on our computer cluster with ClustalW 2.0, with their personal sequences (named with extension ".fasta"; 1000 sequences max.), and/or with sequences directly extracted from PHYMYCO-DB. - Execute an alignment on our computer cluster with their personal alignments (1,500 Ko max., named with extension ".aln") against our pre-computed alignments stored in the database and cross-checked by curators. - For each alignment, an outgroup can be added from a personal file (.fasta) or from our set of outgroup files stored in the database.
- Download fungal sequences using our taxonomic browser.
- Execute an alignment on our computer cluster with ClustalW 2.0, with their personal sequences (named with extension ".fasta"; 1000 sequences max.), and/or with sequences directly extracted from PHYMYCO-DB.
- Execute an alignment on our computer cluster with their personal alignments (1,500 Ko max., named with extension ".aln") against our pre-computed alignments stored in the database and cross-checked by curators.
- For each alignment, an outgroup can be added from a personal file (.fasta) or from our set of outgroup files stored in the database.
Note to users : our interface provides a tool to align sequences with ClustalW 2.0 (Thompson et. al., Nucleic Acids Research, 22: 4673-4680). However, other alignment programs exist and are freely available; please refer to "Alignment uncertainty and genomic analysis, Wong et al., Science 319: 473-476".
Download the whole database content in taxonomy format (can be used with Mothur for example) or in fasta format
How to cite the PHYMYCO-DB ? PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution Stephane Mahe, Marie Duhamel, Thomas Le Calvez, Laetitia Guillot, Ludmila Sarbu, Anthony Bretaudeau, Olivier Collin, Alexis Dufresne, E. Toby Kiers and Philippe Vandenkoornhuyse. PLoS ONE 7(9): e43117. doi:10.1371/journal.pone.004311 Fungal Diversity in Deep-Sea Hydrothermal Ecosystems, Thomas Le Calvez, Gaëtan Burgaud, Stéphane Mahé, Georges Barbier and Philippe Vandenkoornhuyse. Applied and Environmental Microbiology, October 2009, p. 6415-6421, Vol. 75, No. 20
PHYMYCO-DB is now referenced in OMICS Tools and in Database Commons
