On Tue, Feb 5, 2013 at 4:28 PM, Luobin Yang <yangluob@isu.edu> wrote:
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
Thanks Luobin, I've checked that into my development repository (on my tools branch): https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4e... That will allow me to track changes etc as we work on the datatypes. Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy Tool Shed. Regards, Peter