Database Debuts with
Enhanced Access to
Catch the Gene
A Pair of Pathogens
Added to GenBank
Now in Entrez
OMIM In Entrez:
New Searching Power
Slight Address Change
for NCBI FTP Server
PSI-BLAST 2.1 Offers Composition-Based Statistics
PSI-BLAST now permits calculated E-values to take into account the amino acid composition of the individual database sequences involved in reported alignments. Such composition-based statistical analysis improves E-value accuracy, thereby reducing the number of false positive results.
The improved statistics are achieved with a scaling procedure1,2 that employs a slightly different scoring system for each database sequence. As a result, raw BLAST alignment scores will not correspond precisely to those implied by any standard substitution matrix. Furthermore, identical alignments can receive different scores, depending on the compositions of the sequences they involve. The improved statistics are now used by default for all rounds of searching on the Web version of PSI-BLAST, but are not used by Basic or Advanced BLAST. Therefore, if one uses default settings, the results of the first round of PSI-BLAST will be different from those obtained using the same query with Basic or Advanced BLAST.
PSI-BLAST 2.1 is currently available only on the Web, at www.ncbi.nlm.nih.gov/blast/psiblast.cgi. It will be incorporated into the standalone binaries and NCBI toolkit in the near future.
1. Altschul, SF, et al. Nucleic Acids Res 25:3389402, 1997.
2. Schäffer, AA, et al. Bioinformatics 15:100011, 1999.