Stand Alone Blast Exclude without -remote

[tboothby]

Does anyone know if there is a way to exclude certain search perimeters from a Stand Alone Blast?

I know you can do with using the Entrez Query options (either in the web or Stand Alone Version). However, using that option in Stand Alone requires you to also use the -remote option.

This seems to negate most of the benefit of having BLAST set up locally (E.g. you cannot set the number of threads or use custom databases).

Anyone know how to exclude something from a Stand Alone output? Lets say, search a refseq_protein database and exclude anything with "Hypothetical" in the title.

[maubp]

You could prepare a custom database, or go with the traditional approach of filtering the BLAST output in your analysis approach.