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  • Blast query masking behavior

    Hi, this is about a simple alignment issue with NCBI Blast:

    Does anybody know a way to make a query sequence containing masked nucleotides (N symbol) match against the reference region containing an N at the same position?

    For illustration:

    TCNCGCCCCGTGNN | query
    __TCNCGCCCCGTGNN__ | reference (exact copy of query)

    Find the local alignment

    CGCCCCGTG
    CGCCCCGTG


    It does not extend over the whole range of the query even though in my opinion an N should always match and therefore increase the bit score of the local alignment.

    I turned of dust filtering completely.

    Anybody ever happend to avoid this behavior?
    Thanks for any suggestions.

    Gruß Johannes

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