I intend to use a similarity based binning program like MEGAN or SOrt-ITEMS or CARMA for analyzing sequences in my metagenomic data set. For this, I first have to generate a BLASTx output of my metagenomic sequences against a huge data base such as nr or pfam. I do not have huge computing resources to run a standalone for the same. Any suggestions as to how do I obtain a blastx output for a million sequences.
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