Questions tagged [pssm]

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Is there a method/web server to generate Position-specific scoring matrix (PSSM) for nucleotide sequences (DNA/RNA)?

Just like, PSI-BLAST is avaialble to generate a PSSM matrix for peptides, is there a web server where we can generate PSSM for DNA/RNA? I want to find homologous sequences to a given RNA sequence.
3 votes
0 answers
118 views

PSSM Matrix in PSI-BLAST

After running PSI-BLAST one obtains a profile matrix with this header: A R N D C Q E G H I L K M F P S T W Y V How does PSI-...
2 votes
1 answer
114 views

Is it possible to reconstruct an MSA with PSSM?

I am thinking of reconstructing an multiple sequence alignment (MSA) of protein sequences from a position-Specific Scoring Matrices (PSSM). Is it possible? I suppose co-evolution information is lost ...
1 vote
1 answer
565 views

Downloading PSSM file from NCBI PSI-Blast results after the UI update

It used to be easy to download off a results page of a PSI-Blast from NCBI the PSSM (scorematrix). Now I cannot seem to find an asn file that is a scorematrix —<...
2 votes
1 answer
48 views

How to deal with wildcards (N) in sequence logos

This is an open question that came to my mind recently, though it might be that it is not a common use case. The purpose is to find common patterns in a collection of sequences by representing the ...
1 vote
1 answer
3k views

How to interpret a PSSM matrix from PSI-Blast - what do the numbers represent?

PSI-Blast on a sequence returns a PSSM matrix file containing two matrices, one to the left, one the the right, for all amino acids: ...
1 vote
1 answer
2k views

How to get PSSM of protein by protein sequence with python? [closed]

I didn't find way that convert protein sequences in FASTA to PSSM by python, and how to write program in python to find PSSM for our data set ? Maybe better to question how to find PSSM from NCBI ...
4 votes
1 answer
115 views

What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?

I have run psi-blast using the NR database, remotely, with one iteration, for several sequences to calculate an evolutionary profile (PSSM) for each of those sequences. However, many of the PSSM ...