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  • blastn default settings

    Hello,

    I am running blastn locally using BLASTN 2.2.29+ (and have also tried BLASTN 2.2.24+)

    According to the manual, the default word size for a blastn search is 11. However, if I set the word size (word_size) to 11, then I get different results to not setting the word size at all. Generally a less stringent BLAST search when I set the word size to 11. I have to take the word size to 18 to get the same results as not setting the word size.

    I ran the same BLASTn search on the NCBI website, and got the same result as setting the word size to 11. Which is unsurprising. However, it is a little confusing as to why the local version of BLAST is behaving this way. Is anyone able to shed some light on it for me please?

    Here is the manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/

    Thank you in advance for any help that you can provide.

  • #2
    To answer my own question, the NCBI said this:

    When you run blastn, you are by default running megablast, which has a
    default word size of 28. To run blastn with word size 11, add this option:

    task -blastn

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