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Table 6.7. Examples of guest Web sites for performing a database search based on the Smith–Waterman dynamic programming algorithm
Server/program   Reference   Web address
BCM Search Launcher (with programming links to several servers) Baylor College of Medicine
Scanps G.Barton, European Bioinformatics Institute;
Swatb Phil Green, University of Washington
SWsrch DNA Databank of Japan
    A comprehensive list of servers for these types of analyses may be found at
    a MPsearch is an extremely fast implementation of the Smith–Waterman dynamic programming algorithm by J.F. Collins and S. Sturrock, Biocomputing Resource Unit, the University of Edinburgh, distribution rights by Oxford Molecular Ltd. Some versions of the MPsearch algorithm at this site use the same penalty for all gaps, others use gap opening and extension penalties. The former is designed to find similar sequences in which gaps are less important in the alignment, the latter the more distant sequence alignments. Current versions of these programs rank the sequences found by two kinds of scoring systems. A statistical analysis is performed but the scores do not appear to be length-normalized. Hence, the sensitivity of the program may not exceed that shown by FASTA (Pearson 1996).
    b Includes Smith–Waterman and Needleman–Wunsch search algorithms. Calculates statistical significance using extreme value statistics (like FASTA and BLAST).


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