The Clustal Series of Programs for Multiple Sequence Alignment

  • Julie D. Thompson
Part of the Springer Protocols Handbooks book series (SPH)


Sequence comparison or alignment is one of the fundamental tools in molecular biology. Alignments are used to search the sequence databases for homologous proteins, in the identification of conserved regions in a set of related sequences, for twodimensional (2-D)/3-D structure predictions, phylogenetic studies, and so on. The comparison of biological sequences began in the early seventies, with the first dynamic programming algorithm for the global (or full-length) alignment of two sequences (1). Dynamic programming is a rigorous mathematical technique that is guaranteed to find the maximal scoring alignment for any two sequences. The optimal local alignment between a pair of sequences, in which only the highest-scoring subsegments of the two sequences are aligned, involves a simple modification (2) to the Needleman-Wunsch method.


Multiple Alignment Output File Dynamic Programming Algorithm Guide Tree Alignment Parameter 
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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Copyright information

© Humana Press Inc., Totowa, NJ 2005

Authors and Affiliations

  • Julie D. Thompson
    • 1
  1. 1.Laboratorie de Biologie et Genomique StructuralesInstitut de Genetique et de Biologie Moleculaire et CellulaireFrance

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