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Why do I get the message "ERROR:BLASTSet...

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Why do I get the message "ERROR:BLASTSetUpSearch: Unable to calculate Karlin-Altschul params, check querysequence" ?

This will happen if your entire query sequence has been masked by low complexity filtering. You will need to turn filtering off to get hits. For further information on filtering, please read the sections of the BLAST FAQs on "What is low-complexity sequence?" and also "After running a search why do I see a string of "X"s (or "N"s) in my query sequence that I did not put there?"

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