How Set A Pssm (Position Specific Scoring Matrix) When Querying With Blast+?

Question

[bhavanireddy04]

help me out if anyone knows the answer for my question, How to search a nucleotide database using PSSM ( i developed the PSSM using set of protein sequences from query set) Do provide me the command in blast program, im using blast 2.2.27+, i have used makeblastdb command.

[Neilfws]

What have you tried so far? Have you read the BLAST+ documentation?

Answer 1

[Hamish]

To search a nucleotide database with a PSSM using NCBI BLAST you will want to use PSI-tblastn. See:

• Documentation for PSI-TBLASTN in the legacy NCBI BLAST docs for blastpgp
• Problem Running Psi-Tblastn...
• Ncbi Legacy Blast Usage With Tblastn/Pssm

Please note that PSI-tblastn is not recommend in cases where a suitable protein database for use with PSI-BLAST is available. Assuming that you are interested in a specific organism or organisms proteomes you should check to see if completed proteomes exist for your species of interest (see http://www.uniprot.org/taxonomy/complete-proteomes), and use those with PSI-BLAST if appropriate.