Questions tagged [pssm]
The pssm tag has no usage guidance.
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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.
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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 ...
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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-...
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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 —<...
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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 ...
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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 ...
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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:
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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 ...
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