Several new features have been introduced into InterPro since the last publication in this journal in 2000. On the annotation side, InterPro entries have been mapped to Gene Ontology (GO) (10
) terms where a term applies to all proteins matching that entry. Not all entries can be mapped due to low specificity in function or process, but for those that can this provides a powerful tool for automatic large scale annotation of proteins to GO terms. Currently, 4102 InterPro entries have been mapped to 1899 unique GO terms, which results in automatic GO assignment to 405 684 unique proteins in SPTR.
A notable improvement in InterPro has been in the searching capabilities. The sequence search package, InterProScan (11
), has been extended to include all new member databases and data, and the Perl stand-alone version has additional features, including allowance for GO annotation, and the potential to plug in the transmembrane and signal peptide prediction programs TMHMM (12
) and SignalP (13
) respectively. InterProScan is available for interactive as well as email sequence submissions. Additional files, for example a list of all InterPro entries, a list of InterPro to GO mappings and a summary of all protein matches are now available on the FTP site. The text search capabilities have been extended to both a simple text search and an SRS-based (14
) search facility for more complex queries.
InterPro has developed an improved user interface for visualisation of the protein matches in a condensed graphical view derived from the ProDom graphical interface (4
). The consensus domain boundaries are computed, and the resulting protein matches are combined rather than each signature being displayed (Fig. A,B). Parent/child related InterPro entries are collapsed into one line, while domain entries are shown on separate line, thereby providing a simple view of family and domain composition. From this view, all proteins sharing a common domain architecture can be grouped, and the sequences aligned and visualised using Jalview (http://www.ebi.ac.uk/~michele/jalview/
) or DisplayFam (15
). Recently, the general web interface for InterPro has been developed, and changes reflect style changes to the EBI web server. A useful addition to the pages is the option to display them as simple HTML, a printer-friendly version, XML and the default view with or without the menu.
Figure 1 New graphical user interface for viewing protein matches of a particular InterPro entry. (A) Graphical view of representative list of proteins matching IPR000340, in which consensus domain boundaries have been computed for the domain line, and parent (more ...)