Functional Proteomics

Volume 484 of the series Methods In Molecular Biology™ pp 379-413

Protein Multiple Sequence Alignment

  • Chuong B. DoAffiliated withComputer Science Department, Stanford University
  • , Kazutaka KatohAffiliated withComputer Science Department, Stanford University

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Protein sequence alignment is the task of identifying evolutionarily or structurally related positions in a collection of amino acid sequences. Although the protein alignment problem has been studied for several decades, many recent studies have demonstrated considerable progress in improving the accuracy or scalability of multiple and pairwise alignment tools, or in expanding the scope of tasks handled by an alignment program. In this chapter, we review state-of-the-art protein sequence alignment and provide practical advice for users of alignment tools.

Key Words

Multiple sequence alignment review proteins software