title: Multiple protein sequence alignment with MSAProbs.
abstract: Multiple sequence alignment (MSA) generally constitutes the foundation of many bioinformatics studies involving functional, structural, and evolutionary relationship analysis between sequences. As a result of the exponential computational complexity of the exact approach to producing optimal multiple alignments, the majority of state-of-the-art MSA algorithms are designed based on the progressive alignment heuristic. In this chapter, we outline MSAProbs, a parallelized MSA algorithm for protein sequences based on progressive alignment. To achieve high alignment accuracy, this algorithm employs a hybrid combination of a pair hidden Markov model and a partition function to calculate posterior probabilities. Furthermore, we provide some practical advice on the usage of the algorithm.
authors.affiliation: Institut für Informatik, Johannes Gutenberg Universitat Mainz, Mainz, Germany.
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Liu
authors.forename: Bertil
authors.initials: B
authors.lastname: Schmidt
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008390:Markov Chains; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins