Multiple Protein Sequence Alignment with MSAProbs (original) (raw)

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.

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Authors and Affiliations

  1. Institut für Informatik, Johannes Gutenberg Universitat Mainz, Mainz, Germany
    Yongchao Liu & Bertil Schmidt

Authors

  1. Yongchao Liu
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  2. Bertil Schmidt
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Editor information

Editors and Affiliations

  1. Dept. of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
    David J Russell

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© 2014 Springer Science+Business Media, LLC

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Liu, Y., Schmidt, B. (2014). Multiple Protein Sequence Alignment with MSAProbs. In: Russell, D. (eds) Multiple Sequence Alignment Methods. Methods in Molecular Biology, vol 1079. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-646-7\_14

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