Questions tagged [psi-blast]

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4 votes
1 answer
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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 ...
Aalawlx's user avatar
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3 votes
0 answers
120 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-...
Caterina's user avatar
  • 307
2 votes
1 answer
487 views

Error in PSI-BLAST when running psipred locally

I am very new to bioinformatics and Linux and am trying to run psipred locally on Ubuntu 18.04 but cannot get PSI-BLAST to work. I have downloaded BLAST legacy version 2.2.26 and unpacked it, uniref90 ...
Hilda's user avatar
  • 21
1 vote
1 answer
593 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 —<...
Matteo Ferla's user avatar
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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 ...
kInG_-_SaLeH   's user avatar
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: ...
Aalawlx's user avatar
  • 517
1 vote
0 answers
142 views

should I continue the iteration of psiblast if the blast step produced only below threshold sequences?

I used a PSIBLAST (position specific scoring) to detect the similarities between specific proteins and the database of Clostridium. The results did not reveal any similarities above the e value ...
ADHD's user avatar
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