Figure 2

An overview of the data processing performed to determine the positions targeted by microarray probes, PCR primers, peptides, or siRNA/shRNAs and to retrieve/display the exon structures of splice variants. The data processing flow in SpliceCenter is as follows: (1) SpliceMiner is used to pre-compute target positions for common commercial microarray probes. Microarray probe sequence files are submitted to the batch query facility of SpliceMiner, and a results file then indicates the target of each probe in genomic coordinates. The results are loaded into the Probe Position and Microarray table of the mySQL database used by SpliceCenter. (2) EVDB data consisting of a list of the unique splice variants for each human gene are loaded into the SpliceCenter database. Genomic coordinates for each exon are specified by those data. (3) For analysis of RT-PCR, PrimerMatch searches a transcript sequence database to locate the primer target positions that correspond to the PCR primer sequences. PrimerMatch results indicate the target positions for PCR primers in transcript coordinates. (4) The Gene/Variant/Exon tables in the database are queried using the transcript coordinates of the PCR primer. The database results are used to convert PCR primer targets into genomic coordinates. (5) A complete list of the gene's splice variant exon positions and pre-computed microarray probe positions is retrieved from the database. (6) The genomic position information for splice variant exons, microarray probes, and PCR primers is passed to the ImageGenerator to construct the graphical image results.