Dear All
I have downloaded the nr database by this command wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz' and have extracted the file "nr". When I run psiblast to obtain the PSSM matrix. I got this error: BLAST Database error: No alias or index file found for protein database [nr] in search path [D:\Test_Experiment;D:\Data\NCBI\db;]
the command is:
psiblast -query 1_dp.fasta -db D:\Data\NCBI\NR\nr -out 1.txt -num_iterations 3 -out_ascii_pssm 1.pssm
I would appreciate to guide me how I can fix it.
Best Regards Dylan
Thank you for your answer. Is there a method to calculate the PSSM matrix in the webserver? I tried this "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on" (program selection: Algorithm PSI-BLAST (Position-Specific Iterated BLAST)). However, I didn't find the PSSM matrix in the results. This is my first time to use PSI-BLAST, thank you for your help.
From Blast help page:
I have obtained a pssm.asn file. Do you know how to transfer it to a matrix? For example, a 27-length protein sequence was uploaded as the input data to psi-blast server. Finally, I got the pssm.asn file. However, I don't know how to understand the content of this file.
I goolge the pssm matrix, I was told that this matrix contains n(27)-rows and 20-columns. The pssm file generated by psi-blast contains 28-rows and n(27)-columns. This made me confused so much.
I really appreciate your answer. Thx.