How To Interpret The Pssm Output

Question

[pratimagurung12]

Hi everyone,

Can anyone please help me in understanding the PSSM ?

As you can see in the picture, beside the position number there is a sequence(YLPSCTYYVS). I wanted to ask whether the generated PSSM is completely depending only on this reference sequence or the PSI BLAST also considers other sequences in the fasta file to generate this PSSM. How PSI BLAST chooses only one sequence from the whole set of sequences in fasta file?Is there any logic behind that or it chooses randomly?

Thanking you, Pratima Gurung

Answer 1

[Hamish]

While the help for the NCBI PSSM Viewer focuses on the PSSMs in Conserved Domain Database (CDD), which are derived in a slightly different way from those produced by PSI-BLAST, the general principles are the same. Thus the section on the consensus sequence summarises what the sequence shown in the PSSM is. The main difference between the CCD PSSMs and the PSI-BLAST PSSMs is that the scoring in a PSI-BLAST PSSM is relative to the consensus shown as part of the PSSM.

[microbeatic]

It seems like the PSI BLAST generates matrix based on the consensus with the first sequence in the alignment. It just doesn't make sense to base the matrix on the first sequence in the alignment. Any reason. why?

[Hamish]

In PSI-BLAST the reference sequence is the query sequence used as part of the search. Since this is generally what you are looking for this is what you would expect.

[microbeatic]

what if i have a set of sequence rather than just one?