title: EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.
abstract: The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases.
authors.affiliation: Evolutionary Medicine Laboratory, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, Sydney Brenner Institute of Molecular Bioscience, The Mount, 9 Jubilee Road, Parktown 2193, Johannesburg, South Africa, andrew.ndhlovu@students.wits.ac.za.
authors.forename: Andrew
authors.initials: A
authors.lastname: Ndhlovu
authors.affiliation: Evolutionary Medicine Laboratory, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, Sydney Brenner Institute of Molecular Bioscience, The Mount, 9 Jubilee Road, Parktown 2193, Johannesburg, South Africa, Department of Biodiversity and Conservation Biology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Belville, Cape Town 7530, South Africa, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA and.
authors.forename: Pierre M
authors.initials: PM
authors.lastname: Durand
authors.affiliation: Sydney Brenner Institute of Molecular Bioscience, The Mount, 9 Jubilee Road, Parktown 2193, Johannesburg, South Africa, School of Electrical and Information Engineering, University of the Witwatersrand, The Mount, 9 Jubilee Road, Parktown 2193, Johannesburg, South Africa.
authors.forename: Scott
authors.initials: S
authors.lastname: Hazelhurst
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D019143:Evolution, Molecular; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software