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      A comprehensive comparison of multiple sequence alignment programs

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      Nucleic Acids Research

      Oxford University Press (OUP)

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          Abstract

          In recent years improvements to existing programs and the introduction of new iterative algorithms have changed the state-of-the-art in protein sequence alignment. This paper presents the first systematic study of the most commonly used alignment programs using BAliBASE benchmark alignments as test cases. Even below the 'twilight zone' at 10-20% residue identity, the best programs were capable of correctly aligning on average 47% of the residues. We show that iterative algorithms often offer improved alignment accuracy though at the expense of computation time. A notable exception was the effect of introducing a single divergent sequence into a set of closely related sequences, causing the iteration to diverge away from the best alignment. Global alignment programs generally performed better than local methods, except in the presence of large N/C-terminal extensions and internal insertions. In these cases, a local algorithm was more successful in identifying the most conserved motifs. This study enables us to propose appropriate alignment strategies, depending on the nature of a particular set of sequences. The employment of more than one program based on different alignment techniques should significantly improve the quality of automatic protein sequence alignment methods. The results also indicate guidelines for improvement of alignment algorithms.

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          Most cited references 21

          • Record: found
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          The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools.

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            Basic Local Alignment Search Tool

             S Altschul (1990)
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              • Article: not found

              The Use of Ranks to Avoid the Assumption of Normality Implicit in the Analysis of Variance

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                Author and article information

                Journal
                Nucleic Acids Research
                Nucleic Acids Research
                Oxford University Press (OUP)
                0305-1048
                1362-4962
                July 01 1999
                July 01 1999
                : 27
                : 13
                : 2682-2690
                Article
                10.1093/nar/27.13.2682
                148477
                10373585
                © 1999

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