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Old 04-09-2010, 08:03 AM   #1
fungs
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Location: DE/SE

Join Date: Jan 2010
Posts: 10
Default 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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