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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 CCR account.  If you are a researcher and would like an account see here for more details.
 

Tools Developed & Installed at CCR

REDfly  is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). Despite more than 20 years of experimental determination of these elements, the data have never been collected into a single searchable database.  REDfly has an active international user base and averages between 200-250 unique users per month, not including access to the data through other avenues including FlyMine, FlyTF, DroID, and FlyBase.  This is developed in collaboration with Dr. Marc Halfon

The Genomic Data Warehouse (GDW) provides a database for storing and efficient retrieval of sequencing and variant data. It features tools for selecting candidate disease associated variants and for guiding variant/candidate gene selection process and provide assessment on how likely the selected variants/genes are involved in various genetic diseases.

miRdSNP is a custom database that allow the user to explore disease-associated SNPs (dSNPs) on the 3'UTRs of human genes and their special relationship with miRNA target sites.  miRdSNP includes data from computationally predicted microRNA target sites and manually curated dSNPs.  The advanced web interface allows users to perform proximity searches between miRNA target sites and dSNPs by gene name, miRbase ID, target prediction algorithm, disease, and any nucleotide distance between dSNPs and miRNA target sites.  More Information

A tool for exploring information on the process of macromolecule crystallization for use in drug discovery. By utilizing chemical knowledge and laboratory data collected from over 20M crystallization experiments using more than 12,500 biological macromolecules, the rate for successful crystallization can be improved.  xTuition seeks to utilize knowledge of the chemical properties of the salts, PEGS, and commercial crystallization screens used during crystallization to suggest improvements to the process.  This was developed in collaboration with HWI.

GATK Variant Calling Pipeline

CCR has developed a pipeline for Next Generation Sequencing (NGS) variant calling using the latest version of Genome Analysis Toolkit (GATK) available from the Broad InstituteContact our help desk for more information and find out how your group can benefit from the use of this pipeline.


 

Bioinformatics tools installed on CCR servers

CCR provides access to many open source bioinformatics software packages on our systems.  We're also happy to either install, or help you install, software you're interested in using for your research.  For the most up-to-date information on what's available on our systems, run the command:  module avail 
or view the list in our knowledgebase:

NOTE: In search bar, type 'bioinformatics' as a keyword to see all bioinformatics-related software or search for a specific package

 

Support & 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 for more information.