Evaluation Measures of Multiple Sequence Alignments

Multiple sequence alignments (MSAs) are frequently used in the study of families of protein sequences or DNA/RNA sequences. They are a fundamental tool for the understanding of the structure, functionality and, ultimately, the evolution of proteins. A new algorithm, the Circular Sum (CS) method, is presented for formally evaluating the quality of an MSA. It is based on the use of a solution to the Traveling Salesman Problem, which identi es a circular tour through an evolutionary tree connecting the sequences in a protein family. With this approach, the calculation of an evolutionary tree and the errors that it would introduce can be avoided altogether. The algorithm gives an upper bound, the best score that can possibly be achieved by any MSA for a given set of protein sequences. Alternatively, if presented with a speci c MSA, the algorithm provides a formal score for the MSA, which serves as an absolute measure of the quality of the MSA. The CS measure yields a direct connection bet...

• Type: Journal
• Year: 2000
• Where: JCB
• Authors: Gaston H. Gonnet, Chantal Korostensky, Steven A. Benner
• Keywords: Evolutionary Tree, JCB 2000, Multiple Sequence Alignment, Protein