In order to evaluate pattern search tools, I want to search a PROSITE query, e.g. [KR]-x(1,3)-[RKSAQ]-N-{VL}-x-SAQ-{L}-[RKTAENQ]-x-R-{S}-[RK], within a sequence database by "rpstblastn".

Thus, I want to generate a PSSM query database. I know I can generate a PSSM database by "makeprofiledb" command line application.

Everything is OK, except that I need a smp file. I can extract it from cdd.tar.gz file, but, for patterns which are not already present in cdd.tar.gz file, I cannot generate smp files. I want to know how to generate these files.

In summary: I want to generate smp file from a PROSITE pattern like "[KR]-x(1,3)-[RKSAQ]-N-{VL}-x-SAQ-{L}-[RKTAENQ]-x-R-{S}-[RK]". I have two options: 1. Generating smp from the patten itself. 2. Generating smp file from an alignment file, for example fasta alignment files.

Please help me in one of the above questions by command line applications of blast+ applications.