Computational Biology Resource Center
- Relational databases (ENTREZ ENSEMBL, etc)
- Query Forms (BLAST, WUBLAST, etc.)
- Transcription Factor Searches (TF binding prediction)
- Gene Finders (Genescane, etc.)
- Molecular Modeling (SYBYL, Insightll)
- Protein Domain Searches (Pfam, SMART, etc.)
- Primer Design (MT Primer, etc.)
- GeneMesh *
- ArrayQuest *
- MUSC DNA Microarray Database *
* Microarray Analysis: The CBRC cluster computer runs a number of DNA microarray analysis applications including:
GeneMesh is a web-based program designed to relate genes in a query set to descriptors making up the hierarchical structure of the U.S. National Library of Medicine's (NLM) controlled vocabulary thesaurus, Medical Subject Headings (MeSH). GeneMesh accomplishes this by referring to the GeneMesh Database, a unique database of genes associated with MeSH terms.
Other DNA microarray analysis tools developed at MUSC include the following:
ArrayQuest is a web-based program for the analysis of DNA microarray data. ArrayQuest is designed to apply various types of analysis scripts including those written in R to microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or data uploaded to the ArrayQuest center-point web server in a password-protected area. ArrayQuest has been described in an article published in the journal BMC Bioinformatics (Argraves et al., 2005)
The MUSC DNA Microarray Database is a web-based relational database system for archiving DNA microarray hybridization data (raw and normalized) derived experimentation performed through the MUSC DNA Microarray Facility. The database was designed using microArrayDB and uses MySQL server to store microarray hybridization data and metadata such as project information (i.e., investigator contact information, experimental design), cRNA target information and process controlling information. The MUSC DNA Microarray Database has been described in an article published in the journal Bioinformatics (Argraves et al., 2003).