Run PHI-BLAST in BLAST+ standalone

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6.3 years ago

S. Prabhakaran • 0

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 • 2.3k views

ADD COMMENT • link updated 4.9 years ago by liuyuqi2005 • 0 • written 6.3 years ago by S. Prabhakaran • 0

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Via the psiblast command:

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

ADD REPLY • link 6.3 years ago by GenoMax 141k

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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

ADD REPLY • link 4.9 years ago by liuyuqi2005 • 0

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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.

ADD REPLY • link 4.9 years ago by GenoMax 141k

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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,

ADD REPLY • link 4.9 years ago by liuyuqi2005 • 0

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