P-Coffee: A New Divide-and-conquer Method for Multiple Sequence Alignment

Abstract

We describe a new divide-and-conquer method, P-Coffee, for alignment of multiple sequences. P-Coffee first identifies candidate alignment columns using a position-specific substitution matrix (the T-Coffee extended library), tests those columns, and accepts only qualified ones. Accepted columns do not only constitute a final alignment solution, but also divide a given sequence set into partitions. The same procedure is recursively applied to each partition until all the alignment columns are collected. In P-Coffee, we minimized the source of bias by aligning all the sequences simultaneously without requiring any heuristic function to optmize, phylogenetic tree, nor gap cost scheme. In this research, we show the performance of our approach by comparing our results with that of T-Coffee using the 144 test sets provided in BAliBASE v1.0. P-Coffee outperformed T-Coffee in accuracy especially for more complicated test sets.