Hi, Peter, You are right, I thought there was already a datatype defined for PSSM, but it turned out there isn't one yet. I attached a draft tool configuration file for psiblast, it was based on the blastp configuration file, please revise as you like. The options that are specific to psiblast are the following: 1. num_iterations 2. pseudocount 3. inclusion_ethresh Other options should be the same as the blastp program. So a typical command line would be the same as blastp except adding above options if non-default values are used. I can see there are two optional output files, one is the PSSM and the other is ASCII PSSM. Besides using a typical query input, psiblast can take a PSSM file or a multiple sequence alignment file as the input. Luobin On Tue, Feb 5, 2013 at 4:53 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Mon, Feb 4, 2013 at 7:32 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Monday, February 4, 2013, Luobin Yang wrote:
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
Could you give a few command line examples of how you typically use psiblast, focussing in the main options only?
I would find that helpful when putting together a new wrapper - since including all the options right away is overwhelming.
Thanks,
Peter
I suspect we would also need to define another datatype for the PSSM pattern files. That makes things more complicated.
Peter