Protein Multiple Alignment Motivation

To study evolution on the genetic level across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Given a set of biological sequences, a multiple alignment provides biologists with a way of identifying and visualizing patterns of sequence conservation, advancing both evolutionary and phylogenetic studies. Protein alignments in particular have been very useful in predicting protein structure and characterization of protein families. Obtaining accurate multiple alignments, however, is a very difficult computational problem because of the high computational cost and difficulty of evaluation of alignment quality.