Question: How to explain difference between two different calls to PSI-BLAST?
0
gravatar for a.nash
2.3 years ago by
a.nash0
UK - Oxford - University College London
a.nash0 wrote:

Hi all, my first post. My day job is quantum mechanics and computational chemistry on proteins, however, before I'm able to apply either I'm facing a bit of a bioinformatics issue and I require some more seasoned advice.

I am trying to build a homology model from a protein sequence that has yet been catalogued. Through Schrodinger Maestro a BLAST and PSI-BLAST search using its default settings return poor bit-scores. Moving aside from Maestro, I decide to try PSI-BLAST via the NCBI site and via the EMBL site.

Both sites yield different hits, with the NCBI PSI-BLAST throwing up PSSM warnings after the second iteration and showing a very poor bit-score on the top hit after the second iteration. Yet, the EMBL site will happily iterate to a third step yielding some good results e.g., bit-score > 180 (if not poor overall coverage, but where it does cover the identity is approx 40% and similarity approx 50%). What could be the result of the seemingly same tool returning two different sets of results?

Looking through the submission details on EMBL, the settings are: --debug --matrix BLOSUM62 --opengap 11 --extendgap 1 --exp 10.0 --expmulti 0.001 --scores 500 --numal 500 --align 0 --dropoff 15 --finaldropoff 25 -F F --database pdb --preselids

Looking through the submission summary on NCBI, the settings are:

Program blastp <--- threw me at first, but it is PSI-BLAST

Word size 3, Expect value 10, Hitlist size 500, Gapcosts 11,1, Matrix BLOSUM62, Filter string F, Genetic Code 1, Window Size 40, Threshold 11, Composition-based stats 2, Database pdb <---I added this entry in myself, it is not mentioned up in the summary but it was selected>

Per input entry screen, I made as many of the settings as identical as possible, although EMBL's implementation of PSI-BLAST has more parameters to change e.g., dropoff, final dropoff, alignment view, usage mode for PHI-BLAST. Further, the EMBL implementation states:

Position Specific Iterative BLAST (PSI-BLAST) 1) refers to a feature of NCBI BLAST 2.0

And the NCBI PSI-BLAST states:

Program: BLASTP 2.6.0+

I would appreciate any thought as to why I am seeing a different set of results?

Many thanks, Anthony

blast alignment • 942 views
ADD COMMENTlink written 2.3 years ago by a.nash0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1789 users visited in the last hour