blastn default settings

[IanAWarren]

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.

[IanAWarren]

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