• Oracle-based Proteomics Analysis and Annotation Web Interface Tool

MSU: Development of a Oracle-based Proteomics Analysis and Annotation Web Interface Tool. We have developed a relational database schema to capture the output of the MASCOT database search program as well as web based software to load and present this data using a web browser. This software allows users to examine a list of proteins believed to be present in their sample and to examine the supporting evidence. In addition, detailed information is available for each protein identified. Lists can be sorted and filtered on various aspects of the mass spectrometry data and protein attributes. Users can attach comments to individual proteins found in each experiment. Users can also compare results between experiments to identify proteins that are differentially expressed or to obtain confirming data in replicated samples. This tool make possible the analysis of complex data sets that would be difficult or impossible to do by hand and greatly simplifies and speeds the throughput of proteomics results to researchers. Future enhancements to this tool set will be to include additional information about the quality of the MS/MS data to the display page, incorporating the results of de novo sequence determination programs, and to use more sophisticated methods to evaluate the significance of protein identification by the various proteomics analysis software.

• LARALink

WSU: LARALink is a database driven web application, which utilizes several public datasets important for analysis of genetic disorders. LARALink allows UniGene clusters or SNP’s to be queried for multiple patients by cytoband, marker or base pair range.

http://laralink.biosci.wayne.edu:8080/unigene/index.jsp

• Onto-Tools

WSU: Onto-Tools: http://vortex.cs.wayne.edu/Projects.html We developed Onto-Express (OE) as a novel tool able to automatically translate lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. Related tools include Onto-Compare, Onto-Design, Onto-translate, Onto-Miner, and TAQ, which further assist in microarray experimental design and analysis.

• EST Analysis and Databases

MSU Bioinformatics have developed a number of Expressed Sequence Tag tools and databases primarily focused in agriculture that are now available to the state and international community. MCBI funds have supported this effort.

• Full Genome Cluster-Enabled BLAST analysis

Available at UM, MSU, WSU

• Microarray design and analysis

WSU: Affymetrix and spotted microarray analysis Custom Affymetrix chip design MSU: Custom oligo microarray design for animal, plant, and micro-organism genomes Microarray analysis UM: Custom full-genome oligo-nucleotide design

• Bioinformatics analysis, and bioinformatics algorithms design consulting

WSU: bioinformatics analysis and algorithm design promoter analysis MARS analysis MSU: bioinformatics analysis and algorithm design Genome Annotation Annotated EST database construction for animal, plant, and micro-organism genomes Promoter analysis Homolog prediction (for SNP detection) Contig analysis UM: Sim4 Web interface (a cDNA-to-genomic DNA alignment tool).

• Computational Modeling

UM Computational modeling Dendrimer Computational modeling

• Ensembl mirror port access for Michigan users

CONTACT:

Mr. Tom DeKoning, Marketing Manager, CTA Corp CTACorp@vai.org

Brian D. Athey, Ph.D., Director, MCBI bleu@umich.edu