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  • blastn perc_identity on matching region

    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!

  • #2
    You could try to set -gapopen and -gapextend to "0". I'm not so sure it will change the % identity value though..
    savetherhino.org

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    • #3
      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!

      Comment

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