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Run PHI-BLAST in BLAST+ standalone

Dear Friends, I want to do pattern specific search against protein database in Blast+ standalone software. However I couldn't find the command line for PHI-BLAST. Can anyone help me to get the command line for PSI-BLAST in BLAST+ and also input specifications.

                                                     Thanking you

Regards, Prabhu, S

phi-blast; blast
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updated by liuyuqi2005 • liuyuqi2005 • written by S. Prabhakaran • S. Prabhakaran

Via the psiblast command:

* PHI-BLAST options -phi_pattern <file_in> File name containing pattern to search

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written by GenoMax GenoMax

Dear Friends,

I am pretty new here. I tried to save the phi-blast to my Blast+ standalone in windows system, but couldn't. Can anyone help me for it? my current blast version is blast-2.9.0+ for win64.

Thanks

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written by liuyuqi2005 • liuyuqi2005

Please don't use SUBMIT ANSWER to ask new questions.

tried to save the phi-blast to my Blast+ standalone in windows system, but couldn't

What does that mean? Did you specify an output file? Post the complete command you used.

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written by GenoMax GenoMax

Probably my question should be "how to run PHI-blast?". I assumed there is a PHI-blast command line, but I found people also run psi-blast using "-phi_pattern patternFile" option. can anyone help me out?

best,

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written by liuyuqi2005 • liuyuqi2005

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