Bioinformatics
Bioinformatics resources at CCR currently provide users with access to enterprise level genomics packages and software for DNA and protein sequence analysis, database search, gene expression analysis, biological pathway analysis, statistical computing, and inferring phylogenies. In addition to access to software packages, CCR staff, who have extensive expertise in bioinformatics, provide researchers with detailed data analysis support as well as custom software design.
Access to all applications requires a login account. The web portals have separate logins. If you are a researcher and would like to have an account with us, please apply for an account.
Tools
| iNquiry | The iNquiry web portal provides access to over 100 bioinformatics applications for DNA and protein sequence analysis, database search, and statistical analysis, such as EMBOSS, Glimmer, HMMer, MrBayes, BLAST and MPIBLAST. More Information | Ingenuity Pathways Analysis | This bioinformatics package provides extensive analysis and modeling of pathways, molecular mechanisms and biological processes. The application is accessed from the Ingenuity website. New users can request a login to the IPA website. More Information |
| GenePattern | This software package provides over 90 computational and visualization tools for analyzing genomic data. The application is accessed through a web browser. New users can request a login by emailing CCR support staff. More Information | VectorNTI | Software package for DNA and protein sequence analysis, and molecular biology data management. More Information |
| BLAT | A DNA alignment tool similar to BLAST, which uses an index of the genome in machine memory. More Information | GCG | The GCG package provides routines to access, manipulate and analyze nucleotide and protein sequences. This is command line access to Accelrys GCG package. More Information |
| R | R is an integrated suite for statistical computing and graphics. More Information | MATLAB | MATLAB integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. More Information |
In additional to the web portals and packages listed above, many other command line and graphical interface applications are available. Please click here.
Support and Services
CCR provides extensive scientific and programming support to the Bioinformatics community.
Scientific Analysis
Bioinformatics and computational biology support include the development of customized tools and approaches to support faculty led research and advanced data analysis and mining for research projects. Contact Dr. Zihua Hu for more information.
Database Design
CCR provides advanced database support including customized database schema design, import and normalization of data, query optimization and data warehousing. Contact Steve Gallo for more information.
Scientific Programming
CCR's scientific programming staff has expertise in the a number of programming languages including C, C++, Java, PHP, Perl, and Fortran, among others. This group provides custom code, interface and web portal solutions to facilitate faculty led research. Contact Steve Gallo and Robert Leach for more information.
