i want to make a pssm from a fasta file for searching with rpsblast, i have the 2.2.23+ version of blast, so formatdb is replaced with makeblastdb. I have used it to make a database from the genome im using, but not for making a custom pssm. can you help me??
makeblastdb is unable to create rps databases or PSSMs. You the a seperate executable called formatrpsdb to create the database (should be included in your BLAST package, version 2.2.23+).
To create a PSSM, I think you still have to use the old (2.2.23) blastpgp executable and create an ASN.1 output matrix (note: not the standard checkpoint file); all the 2.2.23+ protein BLAST executables accept an in_pssm parameter (so you can do blastp, tblastn, etc.)
On a side note, NCBI offers a large set of PSSMs to download. It might be easier to use these instead of creating your own. Perform a cd-search to see which domain ID your protein of interest has.
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