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Multiple Sequence Alignment

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5.4 Summary

Multiple sequence alignments are often computed for known members of a protein family. The aim is to discover sequence motifs that are conserved across the mem bers of the protein family in order to infer the functionally important protein domains. Like pairwise sequence alignments, multiple sequence alignments can be computed using optimal or heuristic methods. In practice most multiple sequence alignments are computed using heuristic methods. These proceed by reducing the multiple alignment problem to a series of pairwise alignments. The order in which these pairwise alignments are fused into the multiple alignment is crucial for the success of the algorithm. The pairwise alignments of the input sequences are used to calculate pairwise distances. This in turn serves as input data for the construction of a guide tree, which determines the order in which sequences are added to the multiple alignment.

Keywords

  • Multiple Sequence Alignment
  • Multiple Alignment
  • Alignment Algorithm
  • Pairwise Alignment
  • Optimal Alignment

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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5.5 Further Reading

  1. A. Elofsson. A study on how to best align protein sequences. Proteins: Structure, Function, Genetics, 46:300–309, 2002.

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  2. D. Gusfield. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge, 1997.

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  3. M. A. McClure, T. K. Vasi, and W. M. Fitch. Comparative analysis of multiple protein-sequence alignment methods. Molecular Biology and Evolution, 11:571–592, 1994.

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  4. J. D. Thompson, F. Plewniak, and O. Poch. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Research, 27:2682–2690, 1999.

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© 2006 Birkhäuser Verlag

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(2006). Multiple Sequence Alignment. In: Introduction to Computational Biology. Birkhäuser Basel. https://doi.org/10.1007/3-7643-7387-3_5

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