Hi, Peter,

Thanks for pointing them out!

The phi-blast and psi-blast actually share the same binary, both use the
psiblast program in the NCBI BLAST+ tools. When the option -phi_pattern is
used, then it does phi-blast searching.

Best,
Luobin

On Mon, Feb 4, 2013 at 11:14 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang <yangl...@isu.edu> wrote:
> > Hi, Peter,
> >
> > What difficulties did you see to include psi-blast and phi-blast when you
> > were working on the other programs in the NCBI+ suite? I would be
> interested
> > in creating a tool configuration file for each of these two.
> >
> > Thanks,
> > Luobin
>
> Hi Luobin,
>
> At first glance, the binaries for psiblast, rpsblast, and rpstblastn don't
> look too different for wrapping. We would need to define a third loc
> file for the RPS BLAST domain databases (like the existing loc files
> for nucleotide and protein databases).
>
> However, I'm not immediately sure where phi-blast existing with the
> standalone NCBI BLAST+ tools. Do you know?
>
> Peter
>
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