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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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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DOI: https://doi.org/10.1007/978-1-62703-646-7_14
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Publisher Name: Humana Press, Totowa, NJ
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Online ISBN: 978-1-62703-646-7
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