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Multiple Sequence Alignment Methods

Volume 1079 of the series Methods in Molecular Biology pp 211-218

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Multiple Protein Sequence Alignment with MSAProbs

  • Yongchao LiuAffiliated withInstitut für Informatik, Johannes Gutenberg Universitat Mainz
  • , Bertil SchmidtAffiliated withInstitut für Informatik, Johannes Gutenberg Universitat Mainz

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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.

Key words

Multiple sequence alignment Progressive alignment Hidden Markov models Partition function Consistency-based scheme