blastn perc_identity on matching region

[Antonvh]

Hi,

I am using blastn with the -perc_identity option. That way, blastn discards the alignments which do not fulfil a minimum % identities. However, I've just noticed that this option takes into account the gap positions and I would need it doesn't. For example, I would need these 2 sequences to yield an identity of 100%. Is that possible?

ATCGATCGAGGGG

ATCGAT--AGGGG

Many thanks!

[rhinoceros]

You could try to set -gapopen and -gapextend to "0". I'm not so sure it will change the % identity value though..

[Antonvh]

Hi, thanks a lot!

However, what I would need is an option to run perc_identity without considering gap positions. For example, if I do -perc_identity 100, I want blastn to pick the alignment

ATCGATCGAGGGG

ATCGAT--AGGGG

but perhaps there is no such an option available.

Many thanks!