Abstract
The problem of simultaneously aligning a number of sequences is referred to as multiple sequence alignment. We provide a dynamic programming algorithm for multiple alignment which extends the dynamic programming algorithm for global pairwise alignment. We describe frequency based algorithms to align a sequence against a multiple alignment and to align a multiple alignment against another multiple alignment. We introduce the method of 3D profile alignment that allows to align an amino acid sequence against a tertiary protein structure. This method is useful for tertiary structure prediction. As the dynamic programming algorithm for multiple sequence alignment is very time consuming, we provide a useful approximation algorithm and discuss the heuristic method of progressive alignment.
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© 2003 Springer Science+Business Media New York
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Zimmermann, KH. (2003). Multiple Sequence Alignment. In: An Introduction to Protein Informatics. The Kluwer International Series in Engineering and Computer Science, vol 749. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-9210-9_4
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DOI: https://doi.org/10.1007/978-1-4419-9210-9_4
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4613-4839-9
Online ISBN: 978-1-4419-9210-9
eBook Packages: Springer Book Archive