I have a FASTA sequence file with about 10 homologous proteins. What I would like to do is create a PSSM from them and use it to search a transcriptome database.
But how to create it? There is a makemat executable for exactly this task in the NCBI legacy BLAST package which does not seem to have an equivalent in BLAST+.
The new psiblast offers a variety of options (eg. -in_msa, out_pssm) with which it should be possible to create an initial profile, but these two options are dependent on a database or subject sequences (which does not make much sense to me).
What am I missing? Any help is appreciated.
