PupaSuite

PupaSuite identifies and annotates single-nucleotide polymorphisms (SNPs) with predicted effects on transcriptional regulation and protein phenotype to prioritize functional variants for genetic and disease research.

Key Features:

• Functional SNP Analysis: Identifies SNPs affecting transcriptional effects, including variants in conserved regions and those predicted to alter transcription factor binding sites (TFBS).
• User-Defined SNP Input: Accepts user-defined SNPs, including variants not yet mapped in reference genome annotations.
• Functional Annotation: Provides annotations from Gene Ontology and OMIM and reports homologies in other model organisms.
• Haplotype Analysis: Analyzes user-provided data to derive haplotypes and associate them with functional annotations.
• Evolutionary Impact Estimation: Estimates putative effects of polymorphisms using evolutionary information.
• SNPeffect Database Predictions: Incorporates predictions from the SNPeffect database to inform potential phenotypic consequences of SNPs.

Scientific Applications:

• Multifactorial Disorder Research: Supports identification and prioritization of functional SNPs and design of genotyping projects based on predicted phenotypic effects and evolutionary significance.

Methodology:

Integrates pre-calculated predictions and functional annotations from Gene Ontology and OMIM, incorporates SNPeffect database predictions, derives haplotypes from user-provided SNP data, and estimates putative polymorphism effects using evolutionary information.