SAPP-salar: Functional annotation interface for Salmo salar

Introduction The Digital Salmon project is building a mathematical model of the metabolic reaction network of Atlantic salmon. The model will broaden our understanding of metabolic and regulatory processes and how these are connected to changes in the diet, enabling insilico screening of the physiological effects of different feed compositions on salmon. This endeavour requires a comprehensive functional annotation of the recently published salmon genome. To this end we present SAPP-salar, a web interface to the salmon functional annotation. Methods Using the shny package for R we made SAPP-salar a user-friendly web-interface to a SPARQL database generated with SAPP (see box). The database holds genome specific information (such as gene positions and sequences for transcripts or proteins) as well as functional annotation for these sequences, generated by multiple bioinformatics tools such as: InterProScan, TMHMM (prediction of transmembrane helices), WolfPSort (prediction of subcellular location), EnzDP (enzyme commission number prediction) and many more.