Dawn: Rapid large-scale protein multiple sequence alignment and conservation analysis

Understanding of protein structure, function, and disease can be obtained from the analysis of protein sequences evolutionary conservation. Multiple sequence alignments of different isolates, orthologs, paralogs, and functional domains provide essential insights into protein function and structure. Evolutionary conservation level is directly correlated with likelihood of missense mutations´ functional impact. A new conservation characterization tool, Dawn, that aligns sequences based on the Divergence Model of protein evolution can align and characterize large numbers of related protein sequences rapidly. Using this tool, a performance improvement of at least two orders of magnitude improvement over current methods. Dawn is applied to three pressing challenges: identification of antiviral targets for therapeutics, multigene family alignment, and analysis of human missense mutations (variants).