Good morning, I'm a stagiaire and I'm trying to understand how the PSSMs work. I need a psiblast PSSM with ungapped alignments, using a single core.
At the moment I have used this command:
psiblast -db ./db2/uniref50_db.db -out_pssm CDK2.ckp -evalue 0.01 -query CDK2.fasta -out_ascii_pssm PSSM.txt -out CDK2_output -num_iterations 3 -num_threads 4
and I got a pssm that I don't really know how to read (everything I know on the pssm derived from a book). I have basically a matrix L X 40,(L should be the query sequence?) where 40 because I have two matrices side by side, with 20 columns for each. Also at the end of each line I have 2 floating point values. At the end of the file I have this:
K Lambda Standard Ungapped 0.1395 0.3225 Standard Gapped 0.0410 0.2670 PSI Ungapped 0.1835 0.3175 PSI Gapped 0.0561 0.2670
Someone can explain to me what does it mean this output?what are these 2 matrix? How can see if this is good or a fake? What could I do for having a PSSM with ungapped alignement?
Another thing, my professor has told me to try with the blastpgp and to compare the 2 PSSMs saying "What you can do is to run the older blastpgp program and compare the PSSMs (they differ by magnitudes, but trends should be similar).". What does he mean with magnitude and trends? How can I compare 2 PSSMs? Whats should be the difference between psiblast and blastpgp output??
(I know I should ask to him, but I've just started the stage and I would not look like an ignorant)
Thank you very much!