Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix.
BACKGROUND
Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evolutionary relationships by querying a database using an algorithm. However, problems arise when sequence similarity is low. This study presents an algorithm that uses the evolutionary rate at codon sites, the dN/dS (ω) parameter, coupled to a substitution matrix as an alignment metric for detecting distantly related proteins. The algorithm, called BLOSUM-FIRE couples a newer and improved version of the original FIRE (Functional Inference using Rates of Evolution) algorithm with an amino acid substitution matrix in a dynamic scoring function. The enigmatic hepatitis B virus X protein was used as a test case for BLOSUM-FIRE and its associated database EvoDB.


RESULTS
The evolutionary rate based approach was coupled with a conventional BLOSUM substitution matrix. The two approaches are combined in a dynamic scoring function, which uses the selective pressure to score aligned residues. The dynamic scoring function is based on a coupled additive approach that scores aligned sites based on the level of conservation inferred from the ω values. Evaluation of the accuracy of this new implementation, BLOSUM-FIRE, using MAFFT alignment as reference alignments has shown that it is more accurate than its predecessor FIRE. Comparison of the alignment quality with widely used algorithms (MUSCLE, T-COFFEE, and CLUSTAL Omega) revealed that the BLOSUM-FIRE algorithm performs as well as conventional algorithms. Its main strength lies in that it provides greater potential for aligning divergent sequences and addresses the problem of low specificity inherent in the original FIRE algorithm. The utility of this algorithm is demonstrated using the Hepatitis B virus X (HBx) protein, a protein of unknown function, as a test case.


CONCLUSIONS
This study describes the utility of an evolutionary rate based approach coupled to the BLOSUM62 amino acid substitution matrix in inferring protein domain function. We demonstrate that such an approach is robust and performs as well as an array of conventional algorithms.
Evolutionary Medicine Laboratory, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. andrew.ndhlovu@students.wits.ac.za.|Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. andrew.ndhlovu@students.wits.ac.za.
Andrew
A
Ndhlovu
School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa. scott.hazelhurst@wits.ac.za.|Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. scott.hazelhurst@wits.ac.za.
Scott
S
Hazelhurst
Evolutionary Medicine Laboratory, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. pierre.durand@wits.ac.za.|Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. pierre.durand@wits.ac.za.|Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA. pierre.durand@wits.ac.za.|Department of Biodiversity and Conservation Biology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Belville, Cape Town, 7530, South Africa. pierre.durand@wits.ac.za.
Pierre M
PM
Durand
D000465:Algorithms; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D003062:Codon / Q000235:genetics; D016208:Databases, Factual; D019143:Evolution, Molecular; D006801:Humans; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D003062:Codon; D011506:Proteins