3
votes
Accepted
How to deal with wildcards (N) in sequence logos
Since the Position Frequency Matrix is an estimate for the probability to find a particular letter at each position, I think the best way to deal with sequencing errors that result in ...
- 173
1
vote
Accepted
Is it possible to reconstruct an MSA with PSSM?
In short I'm afraid it isn't possible because you lose the linkage per Haplotype which is the core information and vital for any population genetics or phylogenetic analysis.
Position-specific scoring ...
M__♦
- 11.9k
1
vote
Accepted
Downloading PSSM file from NCBI PSI-Blast results after the UI update
Have you tried clicking on the "Back to Traditional Results Page" link in the top right corner? If you're expecting a different interface, that might help work out where to find the right ...
- 13.8k
1
vote
How to get PSSM of protein by protein sequence with python?
We solve our problem and create gitHub repository (bio-protein).
- 31
1
vote
Accepted
How to interpret a PSSM matrix from PSI-Blast - what do the numbers represent?
If you read wiki carefully, you can see that PSSM is calculated in 3 steps. First frequency is calculated (how much times was the amino acid or nucleotide on that location in the motif), from that you ...
- 3,571
1
vote
Accepted
What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?
It means -inf. It has to do with how the PSSM score is calculated.
- 3,571
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