Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

Background: Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution. Results: A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (Functional Inference using the Rates of Evolution), which aligns sequences using the evolutionary rate at codon sites, as measured by the dN/dS ratio, rather than nucleotide or amino acid residues. FIRE was used ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Pierre M. Durand, Scott Hazelhurst, Theresa L. Coetzer
• Keywords: BMCBI 2010, Evolutionary, Evolutionary Rates, Sequence Similarity