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<TITLE>Composition based statistics</TITLE>
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<!-- Changed by: Sergei Shavirin, 7-Aug-2000 -->
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<h1 align="center">Composition based statistics</h1>
<P>
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.
<P>
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.
<P>
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.
<P>
1. <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9254694&dopt=Abstract">Altschul, S.F. et al. (1997) Nucl. Acids Res. 25:3389-3402.</a><BR>
2. <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10745990&dopt=Abstract">Schäffer, A.A. et al. (1999) Bioinformatics 15:1000-1011.</a>
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