Get a CSI-BLAST PSSM
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6.5 years ago
ddofer ▴ 30

I'm trying to get the PSSMs (i.e per=site probability of each AA) for a batch of protein sequences. 

I haven't used PSI-BLAST or CS-BLAST in the past, and am unfamiliar with the exact commands needed to pipe them together, and to get the output.

I'd like to use CSI-BLAST on each sequence, then to run 2 PSI-Blast iterations according to that, then to get the profile/PSSM of each sequence as the output. 

 

I know that CSI-Blast can get a checkpoint via:

> csbuild -i infile.seq -o outfile.chk -D K4000.crf -O chk

 

 - But I don't know how to pipe this to the PSI-Blast, andto get the PSSM as the final output. (For each sequence). 

 

Thanks! 

PSSM CS-BLAST PSI-BLAST Protein • 1.5k views
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