Frequently Asked Questions

  1. Why do I get a different PROVEAN score from my locally installed PROVEAN program and from your PROVEAN web server for the same protein sequence variation?
  2. I got an error message saying "BLAST Database error: No alias or index file found for protein database".
  3. Are the PROVEAN Protein Batch or Genome Variants tools available in the downloadable stand-alone package?
  4. Can frameshift or non-sense mutations be predicted by PROVEAN?

1. Why do I get a different PROVEAN score from my locally installed PROVEAN program and from your PROVEAN web server for the same protein sequence variation?

The PROVEAN scores are computed based on the homologs collected from a database. Thus the prediction results may slighty vary with the protein database used and also the versions of PSI-BLAST and CD-HIT programs. Currently, the PROVEAN web server uses the NCBI nr database (September 2012), BLAST v2.2.24+, and CD-HIT v4.5.4.

2. I got an error message saying "BLAST Database error: No alias or index file found for protein database".

You have to set BLAST_DB up to a database alias filename. For example, if you have nr.pal file under "/local/blastdb/nr" directory, BLAST_DB should be "/local/blastdb/nr/nr".

3. Are the PROVEAN Protein Batch or Genome Variants tools available in the downloadable stand-alone package?

No, they are available only on our web server. The stand-alone package contains only PROVEAN Protein function.

4. Can frameshift or non-sense mutations be predicted by PROVEAN?

As described in our paper (Choi et al. 2012), PROVEAN was validated with single or multiple amino acid substitutions, insertions, and deletions, but not for frameshifts and nonsense mutations. Technically, a frameshift or a nonsense mutation can be described as a substitution or a deletion of long amino acid sequence, but PROVEAN has not been tested with those mutations.