Questions tagged [psi-blast]
The psi-blast tag has no usage guidance.
7
questions
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 ...
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-...
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 ...
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 —<...
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 ...
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
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 ...