Figure 1

A component interaction diagram of the SpliceCenter software. The processes depicted in the figure are keyed to the following steps: (1) The HTML Browser submits a form that contains the user query specifying a gene and a microarray, PCR primer sequences, siRNA sequences, and/or peptide sequences. (2) The HTML request is received by a utility-specific servlet that performs input validation. The servlet calls the Sequence Search class providing the primer, siRNA, or peptide sequence as input. (3) The Sequence Search class runs the open source sequence search tool PrimerMatch [16] to locate complementary sequences within a database of unique splice variant transcripts. (3) PrimerMatch returns hits for the query sequences. The Sequence Search class parses the PrimerMatch results and identifies the best match. (4) Sequence Search Result objects are returned to the servlet. (5) Transcript coordinates for alignment of the hits are converted into genomic coordinates by querying EVDB. Also, the user-specified microarray and gene symbol are used to identify microarray probe positions for the specified gene. (6) Genomic coordinates for each query sequence are packaged into position objects. Microarray probe coordinates are returned in probe-position objects. (7) The user-provided gene symbol (or automatically derived target gene for siRNAs or peptides) is used to query all known splice variants in EVDB. (8) Gene, Variant, and Exon objects are returned. Those objects provide the genomic coordinates of the exons in each unique splice variant. (9) Gene objects and position objects are forwarded in the HTML Request to the PrimerCheck Java Server Page. The JSP is responsible for presentation of search results. (10) The JSP calls the ImageGenerator class, which uses the gene and position objects to construct a graphical image of the splice variants and target positions. To create a graphical output, the ImageGenerator class uses the Java AWT classes, including Graphics2D. Graphical images are temporarily stored on the disk drive on the Tomcat Server. (11) An image tag, complete with a tooltip map, is returned to the JSP for inclusion in the results page. (12) An HTML page with the search results is returned to the user's browser. (13) The image tag on the results page refers to the Image Servlet with a unique ID of the user's result image. The browser automatically requests the image from the Image Servlet. (14) The Image Servlet delivers the PNG format image file and cleans the image file from temporary storage.