My requirement is to generate a PSSM (Position Specific Scoring Matrix) from a given protein fasta sequence against a protein database. I have downloaded and installed the latest version of BLAST+ software and have also updated the "path" environment variable to the bin sub-directory, which has enabled me to run the programs under bin sub-directory from anywhere. After that I downloaded all the 13 files of nr database from the ftp site. I extracted the nr.pal file from nr.00.tar.gz. So I have all the 13 nr.##.tar.gz, the nr.pal file, the protein file in fasta format all under the same directory. Now I execute the command from command line "psiblast -query prot1.fasta -db nr -num_iterations 3 -out_ascii_pssm ascii_pssm.txt" This results in the error "BLAST Database error: Could not find volume or alias file (nr.00) referenced in alias file (F:\workspace\Protein_Secondary_Structure_Prediction_Multi_Class_SVM\testProteins\nr)."