It is often the case that mammalian genes are alternatively spliced; most of the resulting alternate transcript patterns are translated in the cell as isoform protein sequences. We have developed a computational pipeline that characterizes such isoform protein sequences for functional differences. Individual isoform sequences are annotated for presence of signatures such as domains and fingerprints. The pipeline then delineates differences in such signatures among the isoform protein sequences. SpliVaP is the resultant data resource; it contains data on splice-mediated protein isoform sequences, differences in signatures among them, and association to disorders.