VIP: A Functional Annotation Platform of Variants in Animal Genomes

Benefit from the ENCODE project, functional annotation of variants in human or mouse genome is relatively easy, however it is still a huge challenge for other animal species. Here, we developed the software “Variant Integration Prediction (VIP)” to functional annotate variants from animal species with a reference genome by transform and integrate human and mouse ENCODE data. The software has fast mode and deep mode. Fast mode provides intersection of variants with gtf file to classify variants according to their location and related transcripts, output amino acids of different alleles for coding variants and discover potential splicing variants. Deep mode: (1) provides conservation score for most of variants; (2) provides information related to conserved protein domain for missense mutation in protein coding genes; (3) integrate ENCODE data and provide potential transcription factor binding sites and relative score for non-coding variants in defined promoter region and 5’untranslated region; (4) predicted potential microRNA binding sites and a reliable score for variants in 3’untranslated region. VIP also provides visualization interface for the display of variants and annotated features of different alleles. We believe the VIP platform will be helpful for the quick discovery and characterization of important functional variants for animal species.