Where to find BLAST+ default parameters?

Question

[biolab]

Hi, everyone,

I am using BLAST+ to identify homologous genes. I would like to know the default parameters of BLASTN. When typing blastn -h orblastn -help, I could not find detailed default values. On blast+_user_manual.pdf downloaded from NCBI, I could not find these default settings. Could you please do me a favor? I am particularly concern about word_size, penalty score settings, repeat filter, etc. THANK YOU very much!

Answer 1

[Andrzej Zielezinski]

1. blastn (megablast) [for highly similar sequences]

   • word_size = 28
   • match/mismatch scores = 1, -2
   • gap cost = linear
   • filter = low complexity regions

2. blastn -task blastn [quite similar sequences]

   • word_size = 11
   • match/mismatch scores = 2, -3
   • gap costs = existence: 5, extension: 2
   • filter = low complexity regions

You can find this information at NCBI BLAST. If you are running local BLAST with outfmt 0 or 1, you will also see the parameters at the end of your output file.

[Wilford203]

This is incorrect, the default word size for command line blastn is 28, the default of 10 is only for the online blast

[Andrzej Zielezinski]

You're right. I updated my answer. Thanks.

[biolab]

Thank you a.zielezinski. Your information is useful.