EvoDB specifications


Unique identifier OMICS_21036
Name EvoDB
Alternative name Evolutionary rates DataBase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.0
Content license Other
Maintained Yes


Additional information

A python script (evodb_get.py) is needed for retrieving sequences and data from the uncompressed database files.

Publication for Evolutionary rates DataBase

EvoDB citation


Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix

BMC Bioinformatics
PMCID: 4535666
PMID: 26269100
DOI: 10.1186/s12859-015-0688-8

[…] he effect of MSA accuracy on the final alignment was investigated using the heat shock hsp70 (PF00012) domain using nucleotide sequence data corresponding to the manually curated Pfam alignments from EvoDB. Using the MAFFT algorithm and by iteratively increasing the gap open penalty from 0 to 3 in increments of 0.1, we were able to obtain alignments of varying quality and accuracy using the compar […]

EvoDB institution(s)
Evolutionary Medicine Laboratory, Department of Molecular Medicine and Haematology, Faculty of Health Sciences; Sydney Brenner Institute of Molecular Bioscience, Johannesburg, South Africa; Department of Biodiversity and Conservation Biology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA; School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
EvoDB funding source(s)
Supported by the National Aeronautics and Space Administration (#NNX13AH41) and (#SFH13091742708).

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