SimpleIsBeautiful is a novel methodology that aims to improve the
statistical assessment of hits returned from a PSI-BLAST
search to yield better delineation of true and false positives. This approach is based on the hypothesis that 'benchmarking' hits from later iterations against hits
from iteration two where the model is least corrupted should improve
the accuracy of a PSI-BLAST search. Hence, a new figure termed Figure Of Merit (FOM) is calculated by combining E-values of iteration 2 with E-values of the final iteration. This FOM is then used to re-rank-order hits in the final iteration.
The script for the SimpleIsBeautiful algorithm is available for download here.
To learn how to use SIB-BLAST, please read the SIB-BLAST Manual.
If you would like to know more about the SimpleIsBeautiful algorithm, please refer to the following article:
M.M. Lee, M. Chan, and R. Bundschuh, "Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches", Bioinformatics 24 (2008) 1339-1343.