MSACompro: Improving Multiple Protein Sequence Alignment by Predicted Structural Features

Multiple Sequence Alignment (MSA) is an essential tool in protein structure modeling, gene and protein function prediction, DNA motif recognition, phylogenetic analysis, and many other bioinformatics tasks. Therefore, improving the accuracy of multiple sequence alignment is an important long-term objective in bioinformatics. We designed and developed a new method MSACompro to incorporate predicted secondary structure, relative solvent accessibility, and residue–residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. Different from the multiple sequence alignment methods that use the tertiary structure information of some sequences, our method uses the structural information purely predicted from sequences. In this chapter, we first introduce some background and related techniques in the field of multiple sequence alignment. Then, we describe the detailed algorithm of MSACompro. Finally, we show that integrating predicted protein structural information improved the multiple sequence alignment accuracy.