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fungs 04-09-2010 07:03 AM

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__ | reference (exact copy of query)

Find the local alignment


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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