In standalone PSI-BLAST command line interface,what syntax do I use to tighten the search settings to increase the stringency? I'm trying to perform a standalone PSI-BLAST on a 2103 AA query sequence using ten iterations, hopefully to the point of convergence after these ten iterations. It is having the issue of stopping the PSI-BLAST prior to convergence and prior to the num_iterations which I set it to in the cmd line interface.
Alternatively, I was informed that I can perform a command line PSI-BLAST using the PSSM generated from the first five iterations of the original PSI-BLAST which I performed about a month ago for this same query sequence.
Please help, every suggestion is welcome in solving this dilemma :)
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