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I'm new to standalone blast+ and the linux terminal.

I set the bash-profile to load the PATH and BLASTDB for my blast already, but I don't know how to use psi-blast yet.

How can I do the search against db with one query sequence? The file has >400 FASTA sequences. I need to checkout every sequence alone against database. Is it possible to run this job automatic in blast+? (one run in loop for every seq?)

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    $\begingroup$ BLAST takes a fasta file with many sequences as a query. Have a look at the BLAST manual. The running in loop question is off-topic since it is about shell scripting. $\endgroup$ – WYSIWYG Nov 19 '15 at 8:36
  • $\begingroup$ I agree with @WYSIWYG that the manual should be your first port of call, however it is rather crap. If you're comfortable with ruby, perl or python, consider learning about the respective bio module. They all have great BLAST integration. $\endgroup$ – James Nov 30 '15 at 3:20

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