Genomic Software
The Computational Medicine Center specializes in genomic software development, with several applications already in use at Cincinnati Children's Hospital Medical Center, the University of Cincinnati and other institutions. Listed below is a selection of our genomic applications, all of which are freely available to the public.
CisMols Analyzer
CisMols Analyzer is a program that identifies compositionally predicted cis-clusters, which the group has labeled CisMols (Cis-regulatory Modules), that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions. CisMols Analyzer is based on the hypothesis that the presence of a cluster of ortholog-conserved known cis-acting elements in all or many of the co-expressed or functionally related genes predicts that the genes were co-regulated by these elements. Designed to search for regulatory clusters not just in the upstream region of co-expressed genes but also in the non-coding intronic and 5' and 3' flanking genomic regions, CisMols Analyzer could lead to the discovery of probes for genome-wide identification of regulatory regions.
ConCisE Scanner
ConCisE Scanner (Conserved Cis-Element Scanner) is a web-based tool that identifies potential targets of one or more clusters of transcription factors with a defined cis-regulatory target specificity, using human and mouse genomes. It enables you to select one or more transcription binding sites and search all genes in the GenomeTrafac database for clusters containing the selected site(s). Within each cluster, you can view the exact position of each binding site.
PolyDoms
PolyDoms maps synonymous and non-synonymous single nucleotide polymorphisms (SNPs) of proteins onto known functional domains, with the goal of distinguishing the functionally significant and potentially disease-related SNPs from the rest.
POLYVIEW
POLYVIEW is a protein structure visualization server that can be used to generate sequence annotations, such as secondary structures, relative solvent accessibility and physical-chemical property profiles. It can also be used to identify residues involved in protein-protein interactions and highlight other important sites and motifs.
SABLE
The SABLE protein structure prediction server can be used for predicting real valued relative Solvent AccessiBiLitiEs of amino acid residues in proteins, and for improved prediction of secondary structures using evolutionary profiles and the predicted relative solvent accessibility of an amino acid residue as a fingerprint of the overall packing.
SIFT
The Sequence Independent Filtering Tool (SIFT) server can be used for ordering putative models of protein structures and filtering out non-native structures with non-physical packing in order to enhance protein folding simulations and protein structure prediction.
TraFaC / GenomeTraFaC
TraFaC and GenomeTraFaC are companion resources for researchers interested in using a comparative sequence analysis approach to find potential cis-regulatory elements in genes.
TraFaC enables users to search human and murine sequences for transcription factor binding sites in the phylogenetically conserved regions. Results are stored and can be visualized in multiple ways. By obtaining a login account, you also can upload and analyze your own sequences.
GenomeTraFaC contains more than 12,000 human and mouse orthologous gene pairs with a validated RefSeq ID that have been aligned and analyzed using TraFaC and other programs. As with TraFaC, you can generate a graph of the binding sites occurring in both sequences as well as a cis-element hit density image that depicts a moving-window average of the number of shared cis-elements occurring in phylogenetically conserved regions.
