4 votes

Error in PSI-BLAST when running psipred locally

This error could be due to the fact that you are using legacy blast, have you tried using BLAST+ instead? If you wish to use PSIPRED with BLAST+, then use the runpsipredplus script here, rather than ...
Pawan Verma's user avatar
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 ...
gringer's user avatar
  • 13.9k
1 vote

How to get PSSM of protein by protein sequence with python?

We solve our problem and create gitHub repository (bio-protein).
kInG_-_SaLeH   's user avatar
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 ...
benn's user avatar
  • 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.
benn's user avatar
  • 3,571

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