Recently much research effort has been devoted to the discovery of relevant Web services. It is widely recognized that adding semantics to service description is the solution to this challenge. Web services with explicit semantic annotation are called Semantic Web Services (SWS). This research proposes an indexation and discovery architecture for SWS, together with a prototype application in the area of bioinformatics. In this approach, a SWS repository is created and maintained by crawling both ontology-oriented UDDI registries and Web sites that hosting SWS. For a given service request, the proposed system invokes the matching algorithm and a candidate set is returned with different degree of matching considered. This approach can add more flexibility to the current industry standards by offering more choices to both the service requesters and publishers. Also, the prototype developed in this research shows the value can be added by using SWS in application areas such as bioinformatics.