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    SWAPSC: sliding window analysis procedure to detect selective constraints


    Fares, Mario A. (2004) SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics, 20 (16). pp. 2867-2868.

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    Abstract

    Sliding-window analysis procedure to detect selective constraints (SWAPSC) is a software system to dissect the constraints on the evolution of protein-coding genes.The programestimates rates of nucleotide substitutions at specific codon regions in each branch of a phylogenetic tree. The program uses several sets of simulated sequence alignments to estimate the probability of synonymous and nonsynonymous nucleotide substitutions. Thereafter, a statistical analysis is conducted to determine the optimum windowsize to detect selective constraints. Finally, the optimum window size is slid along the real alignment and a test for significance of the estimated number of synonymous and non-synonymous nucleotide substitutions in each sliding step is conducted. A number of friendly useful output files is generated.

    Item Type: Article
    Keywords: sliding window, selective constraints,
    Academic Unit: Faculty of Science and Engineering > Biology
    Item ID: 318
    Depositing User: Dr. Mario Fares
    Date Deposited: 15 Jun 2006
    Journal or Publication Title: Bioinformatics
    Publisher: Oxford University Press
    Refereed: Yes
    URI:

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