Application of PSSMs in Structural-Genomic Analysis

The FID library was applied to the task of predicting the protein folds encoded in complete genomes using the recently developed program IMPALA, which is a modification of PSI-BLAST that effectively reverses the search protocol (Schaffer et al., 1999). PSI-BLAST compares a PSSM to a database of sequences by contrast, a single search by IMPALA is a comparison of a sequence to a library of PSSMs (Fig. 3B). Statistical tests with IMPALA have shown that the theory used for the evaluation of BLAST results is applicable with minimal modifications. 

Distribution of Predicted Protein Folds in Genomes of Bacteria, Archaea, and Eukaryotes 

Automatic Prediction of Protein Folds in Complete Proteomes Using PSI-BLAST-Constructed PSSMs 

The number of genes annotated in this genome is unusually large given the genome size. Thus we suspect that many of the annotated open reading frames are not real genes, which results in an unexpectedly low rate of fold prediction. 

The fold prediction rate achieved in this analysis is an even greater improvement over the results achieved with pairwise alignment methods (Fischer and Eisenberg, 1997 Gerstein and Levitt, 1997) than reported previously (Wolf et al., 1999). By contrast, several more recent studies that applied PSSM-based methods to protein sets from individual genomes have reported similar prediction rates (Huynen et al., 1998 Paw- 

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