**0**wrote:

I am working on a project to evaluate the psiblast converge rates for different queries (from the same protein family). I would like to run psiblast such that it saves the PSSM after every iteration till the search converges. One idea I have to implement this is using shell scripts such that, once I get the psiblast output (PSSM) after nth iteration, run one more iteration starting with this PSSM and the query sequence to generate the PSSM for the n+1th iteration. I'll continue doing this till n+1th PSSM == nth PSSM. I'm still fooling around with a fresh standalone install of BLAST+ on my mac. So, any comments to save PSSMs are welcome.

**3.1k**• written 6.9 years ago by subramaniansk •

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