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  • We designed and developed a new method, MSACompro, to synergistically 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. MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/. Then we developed MSACompro, a new multiple sequence alignment method, which effectively utilizes predicted secondary structure, relative solvent accessibility, and residue-residue contact map together with posterior alignment probabilities produced by both pair hidden Markov models and partition function as in MSAProbs [4]. We tested the MSACompro method against this data with contact predictions.
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