MutaGeneSys (Mutation Genome System) uses genome-wide genotype data to estimate individual disease susceptibility. Our system integrates three data sources: the International HapMap project(hapmap.org), whole-genome marker correlation data (description) and the Online Mendelian Inheritance in Man database (OMIM). MutaGeneSys accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. Our system produces population, genotyping technology, and confidence-specific predictions in interactive time.
AUTOSCAN automatically creates data files, uses MAKEPED (converts pre-linkage format files to linkage format), DOWNFREQ (estimates allele frequencies from pedigree data), and PEDCHECK (Mendelian checking) programs and finally starts statistical analyses via the ANALYZE package. ANALYZE performs parametric linkage analysis (MLINK), nonparametric affected sib-pair analysis (ASP), family-based association analysis (TDT, HRRR), and homogeneity testing (HOMOG). Input files for AUTOSCAN are the pedigree files for all chromosomes,the disease model file, the number of loci file, and the ANALYZE input file.The AUTOSCAN also allows easy handling of several phenotype traits and trait features by only changing the disease model file after each run.
LocusZoom is a tool to plot regional association results from genome-wide association scans or candidate gene studies.Users may generate a single plot using a web form, or many plots using batch mode. The software utilizes LD information from HapMap Phase II (CEU, YRI and JPT+CHB) or 1000 Genomes (CEU) and gene information from the UCSC browser, and will accept SNP identifiers in dbSNP or 1000 Genomes format.
HiTSelect is a software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. HiTSelect provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.