EvoDB: Evolutionary rates DataBase

Evolutionary Medicine Laboratory, Sydney Brenner Institute of Molecular Bioscience

University of the Witwatersrand, Johannesburg

EvoDB version 1.0: December 2014, 13672 Pfam families

Description

EvoDB is a flat file database of Evolutionary rate profiles gapped nucleotide multiple sequence alignments and phylogenetic trees for the Pfam-A (protein family) domain and families database. It consists of 5 datasets:

  1. EvoDB.fire -Evolutionary rate or omega profiles for Pfam family profiles determined using the M2a model using the CODEML program in the PAML suite of software. In addition, we also provide the M1a analysis and future versions of EvoDB will also provide M0, M7 and M8 analysis results.

  2. EvoDB.nuc -Nucleotide alignment for the the Pfam protein family in nexus format.

  3. EvoDB.pfam -Protein family alignments in stockholm format those sequences that are not the nucleotide alignments have been pruned from the alignment.

  4. EvoDB.tree -Phylogenetic trees in newick format.

  5. EvoDB.data -Cross reference mapping information with accession identifiers for Swiss-Prot/TrEMBL(Uniprot) and GenBank used to compile the database.


Citing EvoDB

Ndhlovu,A., Durand,P.M., and Hazelhurst,S. (2015) EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A. Database, 2015.


EvoDB and the FIRE algorithm

EvoDB is also used by the FIRE algorithm to infer protein domain functions.


Copyright notice for EvoDB

EvoDB is licenced under the GNU Lesser General Public License.  

Comments or questions? Send a mail to evodb.emu@gmail.com