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
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