{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.

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, but we have increased the gene sets including the RefSeqGene reference sets, and UniProt proteomes. In addition, we have created new gene sets based on the merge of Ensembl+RefSeqGene+UniProtKB isoforms for each gene.

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 six vertebrate species (human, mouse, rat, pig, chimp, and zebra-fish), and two invertebrate species (fruit-fly and C.elegans).
• The APPRIS WebServer, web server that provides annotations of alternative splice isoforms and identifies principal isoforms for other species (see the list of available species).
• 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 pipeline of APPRIS Database.