Nucleic Acids Research, 2006, Vol. 34, Web Server issue W227 Hence, the method is suitable to analyze datasets where there may be many new folds, such as the complete genomes that serve as input to the resource. In summary, the annotation methods employed by sgTarget allow the identiﬁcation and prediction of a wide range of properties for each putative target. These enable users to ﬁlter and prioritize proteins and genes, generating lists of targets to suit diverse requirements. THE sgTarget SERVER A web-based interface has been developed to interact with the sequence annotation pipeline. This allows users to analyze genomic sequences of interest by submitting them to the server, interact with the resulting data by browsing or search- ing and to select and prioritize targets for structural determina- tion according to their choice of criteria. The interface is available at http://www.ysbl.york.ac.uk/sgTarget/ and its functionality is divided into three main pages: Load, View and Target. Load The Load page allows users to submit their sequences of interest through an anonymous interface. Requests are submitted to the annotation pipeline and processed sequen- tially. Annotations for an average bacterial chromosome ( 5 Mb or 4000 protein coding genes) take 24 h to complete. Users can choose to be notiﬁed of progress by e-mail on initiation and on completion of annotations. Depen- ding on the level and nature of user requests, there may need to be some prioritization and arbitration on the order and choice of which organisms or datasets are annotated. View The View page allows users to analyze the sequence annota- tions performed by the resource. Users can browse through the annotations for a dataset using the Browse function. Here detailed annotations are available for individual proteins, and global synopses are available for the dataset’s character- istics. Browsing the data by protein enables users to inves- tigate the results of all the calculations obtained through the annotation pipeline for a particular gene/protein sequence. This includes gene information, such as GC content and codon usage, protein information, such as function, structure and prevalence predictions, and information on the suitability of the target for structural studies, such as the number of transmembrane, disordered and coiled-coil regions, and the protein’s physicochemical properties. Browsing the data Figure 1. Target page with Select function activated. The menu area (on the left) allows users to choose one or more sequence datasets to target. The work area (on the right) allows users to specify selection criteria. In this example, the Mycoplasma genitalium genome has been chosen for targeting. The selection criteria specify that genes must have a GC content and CAI that is optimal for E.coli, and proteins have no homologues with known structure, are likely to be stable, viable in E.coli for at least 2 h, have at most one transmembrane region, and no fibrous or disordered regions (sgTarget’s default selection criteria). When users click the OK button they are presented with the Rank function, and asked to choose how the target list should be prioritized and displayed (shown in Figure 2).