User: harold.powell

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Posts by harold.powell

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Answer: A: PSSM files - relationship between HHBlits .MTX file and Blast .PSSM file?
... Okay, it looks like I was looking at the wrong program (I'm working on a script that replaces psiBlast with HHBlits). My confusion arose because the "addss.pl" script (which Soedinglab supply but recommend you don't use :-)) produces an MTX file if the input is HMMER format. It turns out that the p ...
written 7 weeks ago by harold.powell0
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PSSM files - relationship between HHBlits .MTX file and Blast .PSSM file?
... I'm looking at the outputs of psi-Blast and HHBlits - each produces a PSSM file, but in different formats, with different numbers. I was wondering if there's a simple one-to-one correspondence between the two (i.e. is it possible to interconvert), or if there's information in one that is not in the ...
alignment hhblits psi-blast written 7 weeks ago by harold.powell0
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Comment: A: hhsearch newby question - creating custom database - no <db>_a3m.ffindex file??
... Thanks for the rapid answer - from what you say (which makes good sense and is pretty well what I would have expected), the Wiki is incorrect because the order of commands I used is the order given in the example in the Wiki. I'll ask the authors for advice... ...
written 3 months ago by harold.powell0
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hhsearch newby question - creating custom database - no <db>_a3m.ffindex file??
... I'm just starting with hh-suite, and trying to create a custom database. I thought I'd start with a single protein and see how things went from there. The instructions in the wiki indicate I should get a file (generically) called <db>_a3m.ffindex or (specifically, in my case) HEWL_a3m.ffindex. ...
alignment written 3 months ago by harold.powell0

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