What dose -s mean?

[DustinChen1986]

python SwiftOrtho/bin/find_hit.py -p blastp -i input.fsa -d input.fsa -o input.fsa.sc -e 1e-5 -s 111111
-s: space seed pattern.
Could you figure out '-s: space seed pattern'?

[Rinoahu]

space seed allows mismatches at specific positions in a seed. For example, -s 11011 means the 3rd position can be any character. You can find a detailed explanation at https://en.wikipedia.org/wiki/Spaced_seed#Example

[DustinChen1986]

Thank you for your explanation. I'll figure it out.