Determining "Specific Hits" on Standalone RPS-BLAST

Question

[lauren.manck]

Hello All

I am using the standalone version of BLAST for the first time and have created a local database of PSSMs to try and identify conserved domains of interest in the genomes of various bacteria using the rpsblast function. Is anyone familiar with an effective way to use the blast output given from the command line to determine a "specific hit" to a conserved domain similar to what you would obtain using the web-based CD search?

Thank you!

[lessismore]

Hi , any progress with this?