Detection of Protein Domains in Eukaryotic Genome Sequences

摘要

Large-scale studies of the origins and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains in the genomes of very diverse organism. Current databases, such as SUPERFAMILY, are not able to provide such quantitative data because of species-specific differences and biases in the existing transcript and protein annotations on which they are based. Here we show that the combination of de novo gene predictors and subsequent HMM-based annotation of SCOP domains in the predicted peptides leads to consistent estimates with acceptable accuracy.