Protein subcellular localization prediction and genomic polymorphism analysis of the SARS coronavirus

The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus (CoV). Several sequences of the complete genome of SARS-CoV have been determined. The subcellular localization (SubLocation) of annotated open-reading frames of the SARS-CoV genome was predicted using a support vector machine. Several gene products were predicted to locate in the Golgi body and cell nucleus. The SubLocation information was combined with predicted transmembrane information to develop a model of the viral life cycle. The results show that this information can be used to predict the functions of genes and even the virus pathogenesis. In addition, the entire SARS viral genome sequences currently available in GenBank were compared to identify the sequence variations among different isolates. Some variations in the Hong Kong strains may be related to the special clinical manifestations and provide clues for understanding the relationship between gene functions and evolution. These variations reflect the evolution of the SARS virus in human populations and may help development of a vaccine.