# Composition based statistics

BLAST and PSI-BLAST now permit calculated E-values to take into account the amino acid composition of the individual database sequences involved in reported alignments. This improves E-value accuracy, thereby reducing the number of false positive results.

The improved statistics are achieved with a scaling procedure [1,2] which in effect employs a slightly different scoring system for each database sequence. As a result, raw BLAST alignment scores in general will not correspond precisely to those implied by any standard substitution matrix. Furthermore, identical alignments can receive different scores, based upon the compositions of the sequences they involve. The improved statistics are now used by default for all rounds of searching on the PSI-BLAST page, but not on the BLAST page. Therefore, if one uses default settings, the results of the first round of searching will be different on the BLAST and PSI-BLAST pages.

In addition adjustments have been made to two PSI-BLAST parameters: the pseudocount constant default has been changed from 10 to 7, and the E-value threshold for including matches in the PSI-BLAST model has been changed from 0.001 to 0.002.

1. Altschul, S.F. et al. (1997) Nucl. Acids Res. 25:3389-3402.
2. Schäffer, A.A. et al. (1999) Bioinformatics 15:1000-1011.