{APPRIS} is a system that deploys a range of computational methods to provide annotations of alternative splice isoforms and identify principal isoforms for vertebrate species. These annotations are based on the modules of the APPRIS Database.

The APPRIS principal isoform for each gene is selected as the principal isoform by combining protein structural information, functionally important residues and evidence from cross-species alignments.

The server has been used to annotate the Human genome as part of the GENCODE consortium but {APPRIS} also has annotations for other vertebrate species. The main data source for {APPRIS} are the Ensembl annotations and sequences.

There are three ways to retrieve annotations for alternative splice isoforms:

• The APPRIS Database, a web database that houses splice isoform annotations and principal isoforms for five vertebrate species (human, mouse, rat, pig, and zebrafish).
• The APPRIS WebServer, web server that provides annotations of alternative splice isoforms and identifies principal isoforms for six other vertebrate species (dog, cat, cow, opossum, chicken and fugu).
• The APPRIS WebServices, a collection of RESTful web services that provides automatic access to annotations from the server and database for the two lists of vertebrate species.

In both the APPRIS WebServer and the APPRIS WebServices, the annotation and analysis is based on the modules in the APPRIS Database.